Maltese Prime Minister Joseph Muscat has accused NGOs operating search and rescue vessels in the Mediterranean of unwittingly encouraging human smugglers to send more people out to sea.

Addressing the Maltese Parliament on Monday evening, Muscat said that while Malta had no problem with NGOs rescuing migrants at sea, it was unacceptable for them to advertise their position outside Libyan waters.

"There are instances when some of these NGOs try to make a political point by attempting to reach migrant boats before the Libyan coastguard even though the people on board may not be in a precarious state," Muscat said.

This, he said, often led to diplomatic disputes as the NGOs would then attempt to find an alternative port to disembark any rescued migrants.

In his statement to parliament about the recent migrant dispute, which saw 49 migrants remain stranded for weeks on two NGO ships, Muscat again insisted that the Libyan coastguard was doing a good job and needed to be allowed to work.

However, the prime minister did acknowledge that more needed to be done to improve the conditions and human rights of migrants kept in Libyan detention centres, an issue Muscat said he had raised with Libyan Prime Minister Fayez al-Sarraj during his visit to Malta last week.