The majority of the refugees made the trek across the Sinai Desert after Egyptian police violently broke up a demonstration outside the headquarters of the United Nations High Commissioner for Refugees, or (UNHCR), in Cairo at the end of 2005.
A year ago at Passover, activists petitioned the Israeli courts, claiming that it was illegal to incarcerate the Sudanese refugees under what is known as the "infiltration law," because it does not allow for individual judicial review.
As a result of that challenge, the government appointed a special investigator, Eldad Azar, to interview the prisoners and make recommendations to the minister of defense on the status of each one.
Of the dozens of cases Azar has reviewed, he hasn't found one that represents a security threat, said Anat Ben Dor of Tel Aviv University, who has been instrumental in challenging the legality of the detentions.
Azar did not return phone calls, and the Ministry of Defense did not respond to repeated requests for an interview.
But in Defense Ministry documents of the cases obtained by JTA, Azar routinely concludes that "the prisoner is eligible under the U.N. refugee convention," meaning the prisoner is a legitimate refugee and not a security threat or terrorist. In the documents, Azar often points out that the prisoner is "held without a proper arrest document" and frequently recommends that the prisoner "should be freed for humanitarian reasons."
Among the cases is UNHCR Case Isr114, a father of three who fled Darfur after being arrested and detained for 10 days, was arrested again in Khartoum, then again in Cairo before fleeing to Israel on April 25, 2006.
Azar concludes: "From the minute he arrived in Israel, there is no returning the prisoner to Sudan, because of the danger that is expected from the authorities if they are alerted that he was in Israel."
In 1985 a coup d'etat brought control of Sudan into the hands of Islamic fundamentalists and Omar al-Bashir, who had fought in the Egyptian army during the Yom Kippur War against Israel.
Based on the documents, a significant number of cases involve sloppy paperwork or lack of due process, Dor said. She has sued for damages on behalf of some of the prisoners and is a principal in the petition before Israel's High Court, which is challenging the legalities of the detentions.
"There have been serious, systemic violations of the basic right to liberty," Dor said.
Her goal, she said, is to free the prisoners and enable future asylum seekers to be able to go directly to the U.N. High Commissioner for Refugees and skip prison.
According to an Israeli Interior Ministry official, "On the one hand, Israel is obligated not to return refugees to a place where their lives are likely to be endangered. On the other hand, the matter raises security-related and diplomatic issues."
Dor has some new, unlikely allies in her efforts to keep the refugees out of prison.
On Jan. 10, two Sudanese slipped under the Egyptian-Israeli border fence and, like hundreds before them, gave themselves up to the Israel Defense Forces. But in what is believed to be a first, the Border Police refused to take them. Reportedly they were fed up with imprisoning Sudanese refugees.
The IDF had intelligence officials check out the two Sudanese and concluded "their intentions are not national [security] and therefore they do not require the services of the Prison Authority," according to a confidential IDF document obtained by JTA.
The Sudanese were dropped off at the Beersheva central bus station by a sympathetic IDF officer, who told them to go directly to the UNHCR office in Jerusalem.
Since then, IDF or Border Police have circumvented the prison services four more times, interviewed the Sudanese themselves, determined they were not a threat and brought them to Beersheva. Individual soldiers gave them bus money to make their way to the UNHCR offices for an interview.
Some involved in the issue say Israel has made it more difficult for the refugees to be resettled to third countries because they were imprisoned in Israel.
Michael Bavli, the UNHCR representative in Israel, said no third country is willing to take the Sudanese refugees, because each country will follow the security lead set by Israel. The thinking would be, he said, that they are imprisoned in Israel, which knows what it is doing security-wise, so they must be a security risk.
Bavli said it was concerns over future resettlement for the Sudanese that spurred those involved in the issue to seek alternative detention, placing the refugees on kibbutzim.
"Within six months on a kibbutz, we'll find them an alternative country, because suddenly they are not criminals who are sitting in Israeli prisons," he said.
Bavli and UNHCR have approached Australia and the United States, among other countries.
Eytan Schwartz of the Committee for the Advancement of Refugees from Darfur, a coalition of groups involved in the issue, said, "The ideal solution" would be twofold: first, to speed up the release of the refugees detained in prison to a kibbutz or a moshav, then grant asylum to at least some of the refugees, while stressing that the move is a one-time deal.
"This would demonstrate Israel's willingness to help a community in distress and comply with the country's moral and international obligations," Schwartz said. "At the same time, Israel should make it clear that the Sudanese refugee problem should be dealt with by the international community and cannot become an Israeli problem."
Schwartz said it is important for the Israeli government "to recognize some of them as refugees, because we believe that unless Israel accepts at least some of them, no other Western nation would be prepared to take the rest of them in."
A U.S. State Department official confirmed that Israel has asked for assistance in resettling the refugees. Despite the quiet fact that 55 "enemy nationals" -- mostly Iraqis -- have been resettled from Israel to third countries, the Israelis "don't want to encourage the arrival of more refugees.""The Israelis are considering a humanitarian solution of absorbing some of the refugees," the official said. "It is a case of burden sharing with other nations, including the U.S."
The United Nations warns against short-term fixes.
"Quite frankly, if by some extraordinary measure the entire current group were resettled to a third country, it would only be a temporary solution," said Astrid van Genderen Stort of UNHCR in Geneva. "Such a measure would certainly encourage further illegal movements from Egypt to Israel and a hazardous journey for asylum seekers and refugees."
Israel and UNHCR would like to discourage further infiltrations by returning Sudanese refugees to Egypt. Israeli Foreign Minister Tzipi Livni has discussed the issue with her Egyptian counterpart. And Eliyahu Aharoni, deputy director of the Immigration Police, testified before the Knesset in late December that "the natural and correct solution is a return to Egypt."
The Israeli government is reluctant to say anything publicly against Egypt's handling of the refugees, since its best-case solution involves a new level of cooperation with the Egyptian government. But the government's position, according to Mark Regev, a Foreign Ministry spokesman, is that "Israel does not have a common border with Sudan, and we are not the first point of refuge."
According to the U.S. State Department official, who asked not to be identified, the Israelis "want to work out a way to return future arrivals to Egypt to discourage them from coming."
Stort confirmed that UNHCR "is trying to facilitate contacts between the two countries to ensure safe return to Egypt as the first country of asylum, with the assurance that no one will be forcibly returned to Sudan."
The refugees and activists on their behalf take issue with this approach.
"We should not talk about Egypt as a 'first country of asylum,'" Ben Dor said, "because Egypt doesn't even have an asylum system of its own and UNHCR has advised European governments not to consider countries like that to be safe for returns."
UNHCR has asked Egypt repeatedly to assume responsibility for refugees, even to issue work permits for them, but the Egyptians have refused.
"Egypt is under no obligation to take the Sudanese back," Ben Dor said. "It has been refusing since the end of 2004. Return to Egypt is a dangerous fantasy that distracts from finding a real solution."
At the same time, the Israeli government doesn't have much faith that UNHCR will be able to resolve the situation.
According to an internal Justice Ministry memo obtained by JTA, the attorney general convened a meeting of the army, intelligence and other government agencies to develop a strategy to deal with the Sudanese refugees, including "hot returns" or the immediate return to Egypt of anyone who slips illegally across the border.
"There is no impediment to returning an infiltrator to Egypt, and such a measure requires neither a court order nor any other proceedings," according to a summary of the meeting.
The minutes further reveal the government's attitude toward UNHCR: "They are unable to provide a feasible solution."
For Ahmed, a Sudanese refugee who has been in Israeli prisons since he slipped under the border in late December with his wife and three children, his desire is clear.
"I would rather remain here forever than return to Sudan or to any Arab country," he declared.
JTA correspondent Ron Kampeas in Washington contributed to this report.
Yosef Israel Abramowitz is an award-winning journalist and founder of socialaction.com. Abramowitz, who moved with his family last year to Israel, blogs daily at peoplehood.org. JTA correspondent Dina Kraft in Israel contributed to this piece. The names of the refugees have been changed to protect them from reprisals against family members in Arab countries.