Under legislation passed last month which has sparked mass protests by Africans in occupied lands, people who arrive illegally can be detained for up to a year without trial.
But Adrian Edwards, spokesman for the UN high commissioner for refugees, warned that the new rules could enable indefinite detention.
Israel has also opened a sprawling detention facility at Holot in the Negev desert to house both new entrants and immigrants already in the country deemed to have disturbed public order.
"Since Holot is housing people who cannot be returned to their countries of origin for reasons to do with non-forced returns, we're concerned that this facility will in effect result in indefinite detention with no release grounds," Edwards told reporters.
"Indefinite detention certainly would be at odds with human rights norms," he added.
Israel's right-wing government has vowed to step up the repatriation of illegal immigrants, saying they pose a threat, but critics counter that the country is not giving genuine asylum-seekers a fair hearing.
Israel currently hosts approximately 53,000 refugees and asylum-seekers, according to UNHCR.
Most managed to cross the desert border with Egypt, before Israel completed a barrier last year.
Some 36,000 come from Eritrea, whose regime repeatedly has been accused of widespread human rights abuses by the international community.
Another 14,000 are from conflict-torn Sudan.
NJF/NJF