Rwanda and Uganda, which had offered to settle African refugees in Israel, are now grappling with a new order by Tel Aviv that the illegal immigrants must leave the country within 90 days or be jailed.
Israel's Prime Minister, Benjamin Netanyahu has told African immigrants in his country to voluntarily go back to their countries of origin or third country risk being repatriated forcibly, or jailed.
According to reports by Israeli media, PM Netanyahu said the plan to expel unwanted African immigrants 'is already underway', with a 90-day ultimatum issued for all refugees to have left or be jailed.
Mr Netanyahu has asked authorities to "examine the feasibility of forcibly deporting the thousands of African migrants" to their respective countries or a third country, which has been confirmed as Rwanda and Uganda.
According to reports, Uganda was one of two African countries -- the other being Rwanda -- prepared to accept the migrants if they refused to return to their home countries.
But, in a new twist, Uganda's State Minister for Foreign Affairs and Co-operation, Henry Okello Oryem said that they are 'baffled' by reports of the deal to accept thousands of African migrants being expelled from Israel.
He told the Daily Monitor that no such deal had been reached with Israel, which is ordering Africans it labels "infiltrators" -- meaning those who did not enter the country through an official border crossing -- to leave within 90 days.
"We have no agreement with the Israeli government to send refugees from other countries that are in Israel to Uganda. We are baffled by the reports. We have no partnership agreement with the government of Israel. Ask them (Israel) to explain how they reached that decision," he said.
Addressing the Cabinet last week, Mr Netanyahu said that the mission is to expel the 40,000 'infiltrators' mainly from Sudan and Eritrea, who reportedly entered Israel over a decade ago before the country constructed a barrier along its border with Egypt.
"Today the Cabinet will approve the plan for deporting the infiltrators from Israel. We will step up enforcement and we will allocate budgets and personnel to implement the plan. I think that it is important that people understand that we are doing something here that is completely legal and completely essential," he said.
The deportation has come under scrutiny by human rights groups which accuse Israel of violating the rights of the refugees and putting their lives in danger. Tel Aviv is accused of paying the two African countries to accept the refugees.
President Paul Kagame has in the past admitted that Rwanda and Israel were working together to address the refugee problem.
Latest reports, however, say that Rwanda deputy Foreign Minister, Olivier Nduhungirehe, told the Associated Press that his country has never reached any agreement with Israel on hosting asylum seekers.
Both the Ministry of Foreign Affairs and the Immigration Directorate have refused to divulge details of this deal, which according to reports would have seen Rwanda receive at least 10,000 of the deportees, each paid between $3,500 and $5,000 to leave. The recipient governments were supposed to receive $5,000 per immigrant that they take in.
Uganda denies being party to the deal despite human rights groups in Israel maintaining that it has already secretly received a considerable number of deportees from Israel.
The immigrants have expressed fears of returning to their home countries, and that their safety and wellbeing is not guaranteed in third countries.
Many of them say they are unable to return as they came to seek asylum after fleeing persecution and conflict.
Unofficial reports say that there are some 38,000 migrants living illegally in Israel, and some 1,420 are being held in two detention centres.
Rights groups such as Centre for Refugees and Migrants, Amnesty International Israel and the Association for Civil Rights in Israel have signed petitions to block the deportations despite courts and parliament giving them a go ahead.
"Anyone who has a heart must oppose the expulsion of the refugees...Rwanda is not a safe place. All the evidence indicates that anyone expelled from Israel to Rwanda finds himself there without status and without rights, exposed to threats, kidnapping, torture and trafficking," the watchdogs say.
Dror Sadot, a spokeswoman for the Hotline for Refugees and Migrants told The EastAfrican that while the government continues to call them 'infiltrators', the refugees are legitimate asylum seekers fleeing genocide, political persecutions and rights abuses.
By Fred Oluoch, Edmund Kagire and Agencies