A group of 110 people may be unaccounted for with emergency services NGO Alarm Phone accusing the Armed Forces of Malta of ordering a rescue vessel to leave the scene of the drifting boat the migrants were in.
A Seawatch International spokesperson confirmed that the third boat has not yet been rescued.
A merchant vessel, Nordicstar was in the vicinity of the third boat and had agreed to rescue those onboard.
"We were informed by the captain of the Nordicstar that a Maltese patrol boat stopped the vessel from rescuing the boat and forced it to leave the scene," the Seawatch spokesperson said.
He said that his NGO and Alarm Phone had not received any news of the boat since and there is no sign of it in the Maltese SAR zone.
"There are two possibilities - that Maltese patrol boats rescued the ship, which is unlikely, or that they forced a pushback. It is too early to say."
Meanwhile, efforts to contact the Armed Forces of Malta proved futile.
On Saturday, NGOs had reported sighting three boats with migrants adrift in Maltese SAR zones, with a total of around 270 people on board.
In the evening, Alarm Phone said that migrants on two of the three boats had been taken to Lampedusa.
The third, it said, remained south-west of Malta, despite merchant vessels captured on camera in the vicinity of the boats and the AFM being aware of the situation.
On Sunday, Alarm Phone said it had no information on the fate of the remaining 110 people.
“According to the Moonbird crew, Armed Forces MT was with the boat and ordered to Nordic Star to leave the scene. The people never arrived in Malta. What happened to them?”
Government should explain its silence - CSN
In a statement, Civil Society Network demanded an explanation from the government.
"CSN is demanding an explanation from the government regarding the fate of 270 people who were reportedly in distress in Malta's search and rescue zone," it said adding that, so far, there had only been the usual silence.
The NGO reminded the government that it was responsible for protecting the lives of everyone in its jurisdiction.
"The established SAR zone, while not instructive of where to disembark rescued people, obliges the state to coordinate the rescue of imperilled lives, irrespective of their identity or nationality," CSN said.
In another statement, NGO Repubblika urged the Maltese and Italian authorities to intervene, warning of a repeat of last year’s Easter incident.
Last year, a delay in rescues over the Easter weekend ended in a number of deaths and a pushback orchestrated by the Maltese authorities.