"Libya is an unsafe port where migrants should never be brought back," Flavio Di Giacomo, a spokesman for the UN's International Organisation for Migration wrote on Twitter.
He told Reuters there were 485 migrants and they docked in the Libyan port of Benghazi on Friday.
Alarm Phone, a group that picks up calls from migrant vessels in distress, had no signs from the boat since Wednesday morning.
At the time, the boat was adrift, with no working engine, in high seas about 320 km north of Libya and more than 400 km away from Malta or Italy's southern island of Sicily.
The Italian Coast Guard reported on Thursday the rescue of 423 and 671 migrants in two separate operations in Italian search and rescue waters, and Alarm Phone said they were unrelated to the missing boat.
In a separate incident, German charity SOS Humanity said 27 migrants were picked up at sea by an oil tanker and illegally taken back to Libya.
Under international humanitarian law, migrants cannot be forcibly returned to countries where they risk serious ill-treatment. Widespread migrant abuse has been extensively documented in Libya.
European governments have taken an increasingly hard line on migration, including in Italy, which is facing a surge in sea arrivals. More than 47,000 landings have been recorded in the year to date, up from around 18,000 in the same period of 2022.
