Sudanese asylum seekers in Israel are being issued with documents changing their nationality, allowing them to be removed from the country or imprisoned.

They have recently been issued with documents labelling them as South Sudanese – despite holding passports showing they were born in areas that remain in Sudan.

Four migrants from the Republic of Sudan have already been flown from Israel to South Sudan, an entirely different country that was formed last year. However, the South Sudanese authorities refused to accept them at the border and they were sent back to Tel Aviv.

Non-governmental organisations (NGOs) estimate that at least 100 more Sudanese asylum seekers in Israel may have been issued with the wrong nationality in the past three months, and fear there may be more attempts to remove them.

South Sudan came into existence only in July 2011 after a 21-year civil war. Intense hostilities remain between the newly formed country and the Republic, with conflicts regularly breaking out on the border.

Israel is unable to deport people to Sudan as it has no repatriation agreement with Khartoum. But a recent deportation order allows it to deport migrants to the country's newest neighbour, South Sudan.

Now, NGOs based in Israel report that people from the Nuba mountains region of Sudan are being issued with temporary visas stating they are South Sudanese by the Israeli ministry of the interior, making them eligible for removal from the country. South Sudanese asylum seekers have been asked to leave Israel voluntarily, but those who do not face imprisonment.

Thomas Abdallah Tutu, 32, who lives in Arad, in the south of Israel, is one such case. He is from the Nuba mountains in Sudan and arrived in Israel in 2007. Mr Tutu recently had his documentation recalled and was issued with a temporary visa for Israel that gave his nationality as South Sudanese.

Now he fears he will lose his job as a hotel steward, and could be imprisoned and flown to South Sudan.

The prospect of moving to South Sudan, which even before secession was in conflict with Sudan, is worrying for migrants. "It is a bad situation in South Sudan", Mr Tutu told the Bureau of Investigative Journalism in a phone call. "There is nothing there and no one has family, houses or money. They are afraid to go, and confused," he said. "If I go there I am sure something bad will happen to me."

The African Refugee Development Centre, an NGO based in Tel Aviv, which works with African migrants, has seen around 70 people with passports and birth certificates suggesting they are Sudanese, who have been given South Sudanese documentation. It estimates the number of those affected may be twice that. The UNHCR (the UN refugee agency) and two other Israeli NGOs, the Hotline for Migrant Workers and Students for Refugees, also reported witnessing Sudanese migrants being issued with South Sudanese documentation and being imprisoned or coerced into leaving Israel.

Peter Deck, senior protection officer at the UNHCR in Tel Aviv, said: "There have been cases of confusion of persons from Nuba mountains and Darfurians considered as from South Sudan who had their visas taken away."

Paul Hirschson, a spokesman for the Israeli ministry of foreign affairs, explained how the confusion arose. He said: "The vast majority of people arrived in Israel before South Sudan existed. We've been working very closely with South Sudan to identify who is South Sudanese." He added that it is the South Sudanese government's responsibility to issue passports and travel documentation.

The UNHCR has voiced concerns over Israel's immigration policy. "The return taking place from Israel to South Sudan does not meet UNHCR standards outlined in the formulated UNHCR guidelines for voluntary return," Mr Deck said.

Several NGOs report that children have been imprisoned in unsuitable conditions, people are given insufficient time to make preparations, and some are imprisoned despite having signed up to "voluntary departure".

African migrants are an issue of concern for the Israeli government. According to the ministry of foreign affairs there are approximately 60,000-65,000 illegal immigrants in the country. However, two-thirds of those come from Eritrea, Somalia and Sudan – countries which Israel cannot repatriate citizens to, due to their collective-protection status.

Confusion over nationalities has occurred before. The Israeli newspaper Haaretz reported how the government used a loophole to deport people from Eritrea to Ethiopia based on an Eritrean law granting citizenship to anyone whose mother or father was an Ethiopian citizen. The rule change allowed the Israeli government to deport Eritreans to Ethiopia, claiming that they could obtain citizenship there.

The ministry of foreign affairs categorically rejects the notion it is using vagueness around nationalities to allow for the removal of some Sudanese to South Sudan.