A United Nations agency has voiced alarm after a migrant boat stranded in Maltese waters carrying 49 people was returned to Libya, where hundreds have gone missing since the start of the year.

The International Organization for Migration said it was “alarmed by this apparent breach of international law”, after the wooden boat was sent back to Libya on Sunday. Returning vulnerable people to Libya would breach a cornerstone of international law, against returning asylum seekers back to countries where they risk persecution, a principle known as non-refoulement.

“Libya is not a safe port and that is recognised by the UN and other European states,” said a spokesperson for IOM, Safa Msehli. “The return of people from Maltese waters – of which we have confirmation from various sources – is a breach of international law and we would like to remind states of their responsibility towards vulnerable people that are fleeing abuse and violence in Libya.”

Rights groups and others accuse the European Union of having a policy towards Libya that sustains a network of detention centres in the north African country, where people are kept in “inhuman and degrading conditions”.

Libya’s coastguard, which receives EU funding and equipment, has returned more than 2,500 people to its shores since the start of the year. The IOM said it was worried about 600 people picked up at sea and sent to a centre in Tripoli, which is under the control of Libya’s interior ministry. Libyan authorities have failed to respond to requests for information about what happened to these people, the IOM said.

“The worry for the safety of these people is obviously there, because we don’t know their fate and they could have been smuggled,” Msehli has said.

Last year, the UN raised concerns that migrants rescued at sea and returned to an unofficial detention centre in Khums were being sold by Libyan police to smugglers and traffickers, or simply disappearing.

The UN refugee agency estimates that Libya hosts more than 43,000 refugees and asylum seekers, in addition to 217,000 people displaced by conflict. An estimated nine in 10 people attempting to reach Europe by sea start their journey in Libya.

Since the start of the year more than 2,700 people have reached Italy, while nearly 1,000 have arrived in Malta, the EU’s smallest member state.

The UN has been urging the EU for months to set up a scheme that allows people rescued at sea to disembark safely in Europe and apply for asylum – something EU leaders promised in June 2018.

But the plan has been stymied by a general lack of political will and anti-migrant politicians, such as Matteo Salvini, who turned away boats from Italy while he was the country’s deputy prime minister.

A spokesperson for Malta’s interior ministry said international law had been observed at all times. “In fact, contrary to the claims being made, Malta rescued 112 irregular migrants during the same period that is being referred to,” a point made in the IOM’s original statement.

The spokesperson added: “The Maltese authorities remain committed to reducing the loss of lives at sea.”