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The programme is targeting an estimated 38,000 people, mainly from Eritrea and Sudan.
Israel has offered them $3,500 (2,900 euros) and a plane ticket if they leave by March, warning they may face arrest after the deadline.
The plan was widely criticised when first unveiled last year, but the UN refugee agency sounded a fresh alarm after Israeli Prime Minister Benjamin Netanyahu’s announcement last week that the programme had begun.
“UNHCR is again appealing to Israel to halt its policy of relocating Eritreans and Sudanese to sub-Saharan Africa”, the agency said in a statement.
UNHCR spokesman William Spindler told reporters in Geneva that the programme was not “coherent” and “has been implemented not in a very transparent manner.”
Israel has not clearly said where the migrants will go, but tacitly recognises it is too dangerous to return the Sudanese and Eritreans home.
As a result, according to activists in Israel, it has signed deals with Rwanda and Uganda, which agree to accept departing migrants on condition they consent to the arrangement.
Uganda has publicly denied any such deal. Rwanda has also dismissed its involvement, according to the UN.
Spindler said the fact that the purported host countries were denying their role made it impossible for the UN to follow up.
UNHCR said it had spoken to 80 people who were flown with the $3,500 to Rwanda before heading north, travelling to Rome through conflict zones in South Sudan, Sudan and Libya.
“Along the way they suffered abuse, torture and extortion before risking their lives once again by crossing the Mediterranean to Italy”, UNHCR said in a statement, explaining that its staff interviewed the migrants in Rome.
Spindler called on Israel to find alternative solutions to the problem, stressing that the UN was ready to help with formal resettlement through official channels.
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