The global body's refugee agency UNHCR said on Thursday that 100 people were "unaccounted for" after being taken to the border, while 20 others remained "stranded in the desert".
It said the group of Syrians, Palestinians and Yemenis had been detained in southern Algeria before being taken to an area near the Guezzam border post on 26 December.
Hacen Kacimi, an Algeria interior ministry official, said the expulsions took place after legal decisions "closely linked to national security priorities".
"No party, irrespective of its status, can interfere in the execution of a judicial decision," he added.
Kacimi, who heads the ministry's migration department, had previously said the migrants entered Algeria illegally and were put on trial in September.
Algeria does not have asylum legislation and the official said many of the migrants - mostly Syrians from Aleppo - were suspected of having ties to jihadist groups.
Kacimi on Friday accused UNHCR of "erratically" registering asylum applications, after the agency said some of those expelled were registered refugees.
Defending the expulsion at the remote desert border, Kacimi said the group "refused to be repatriated by air".
Human rights organisations regularly criticise Algeria for its treatment of migrants, many of whom come from sub-Saharan Africa in the hope of reaching Europe.
The UN in October urged Algeria to stop collective expulsions of migrants across its Niger border, after rights groups accused authorities of rounding up thousands of people and expelling them into the desert.
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