The refugees, assuming they will be granted asylum, usually wait to be picked up by the IDF after crossing into Israel. However, the security forces arrest them for illegal entry and, in virtually all cases, place them in detention centers. Currently at least 198 Sudanese are detained in Israel.

Sudanese asylum seekers and refugees are not being deported to Egypt, due to fears, based on previous incidents, that they will subsequently be deported to Sudan. However, the government refuses to allow them to even apply for asylum. It bases its refusal on the fact that they are allegedly from an "enemy country" and therefore are presumed to be “dangerous to State security.” The status of being from an "enemy nation" is inclusive; the State does not check individual cases to verify that they are actually dangerous in any way.

The treatment of Sudanese in Israel contrasts with the way Israel handles asylum applications from other nationalities. Recognized refugees in Israel are released from prison and granted work and stay permits as well as social benefits. Asylum seekers whose cases are in the process of review are similarly released and given temporary work permits.

Israel's treatment of Sudanese asylum-seekers violates several bodies of international law, which Israel has signed and ratified. Human rights and refugee law (mainly grounded in the 1951 refugee convention) prohibits discrimination on the basis of national origin in asylum policies and forbids states from singling out particular nationalities for disadvantage as related to immigration. The Fourth Geneva Convention of 1949 requires that states exempt refugees from the measures they might otherwise take against enemy nationals. Ironically, this last provision of international humanitarian law was promoted by the young State of Israel, remembering that the UK had sheltered German Jews during World War II even though they were citizens of an enemy state.

At first, the cases of Sudanese entering the country were handled by the Ministry of Interior and the Immigration Authority (IA). They were detained in IA prisons under the Law of Entry to Israel as are all undocumented migrants. Because they cannot be deported, the UNHCR in Israel, the Refugee Rights Clinic and the Hotline for Migrant Workers, were able to release some of the first arrivals to various Kibbutzim in Israel. This was done on a case by case basis through an agreement reached with the Ministry of the Interior. Later, when the Ministry of Interior began to refuse their release, we successfully petitioned the Tribunal for the Review of Custody of Undocumented Migrants for their release. Some 30 asylum seekers were released in this manner.

However, in early 2006, the State began to deny Sudanese refugees the rights that even undocumented migrants are entitled to. Rather than detaining them under the Law of Entry to Israel, they are being held under an emergency law enacted in 1954, called the Prevention of Infiltration Law. A draconian law, it allows for unlimited detention, without judicial review, of a person who is either a national of one of the countries enumerated in the law (Sudan is not included) or who have passed through one of those countries. Egypt, despite being officially at peace with Israel, is included in this outdated law. Because the refugees have entered Israel via Egypt, technically, they can be detained as infiltrators.

In response, the Hotline for Migrant Workers and the Refugee Rights Clinic at Tel Aviv University filed High Court petitions against the use of the Infiltration Law in four cases. A hearing on these cases was held on Monday, May 8, 2006 and the State was ordered to provide judicial review in detention for Sudanese within 30 days. However, regular judicial review for all of the detainees, including those located in the far south of the country, only began in December following another legal petition filed by the organizations.

In addition to legal action, the Hotline for Migrant Workers continues to assist the refugees in other ways. Volunteers regularly visit detention centers. They take the testimony of the refugees and provide them with humanitarian aid such as donated clothing and phone cards. Volunteers also assist them in accessing medical treatment and maintaining contact with their families. The Hotline for Migrant Workers has identified placements on kibbutzim and moshavim for all of the detained refugees- and has managed to release some of those detained under the Law of Entry into Israel to kibbutzim. However, the vast majority, defined as enemy infiltrators by the State, continue to languish in prison- some for over a year.

The Hotline is working with other NGOs and the Israeli government to formulate a long-term solution. They established the Committee for the Advancement of Refugees from Darfur (CARD), consisting of a diverse group of seven NGOs concerned about the issue. Chaired by esteemed Yad Vashem Holocaust researcher Yehuda Bauer, CARD has identified two members of Knesset (one from left-leaning Labor and the second from right-leaning Likud) to work with the government.

The long-term fate of the Sudanese refugees in Israel is yet unknown. According to various declarations made by the government, Israel will not provide a safe haven for Sudanese refugees. A delegation from UNHCR-Geneva is currently conducting an individual assessment of all cases, and might opt for resettling the refugees in a western country. However, this process is long and resettlement is not guaranteed. Various Israeli officials expressed their hope that the refugees would be returned to Egypt, following negotiations which are currently underway, despite doubts regarding the effectiveness and quality of Egyptian protection. Pending legislation would prevent the release of any enemy national, including Sudanese, effectively sentencing them to a future without hope.