Updated 7.15pm
A merchant vessel has picked up the 90 people in distress in Malta's search and rescue area, Alarm Phone has tweeted.
Earlier, the NGO said that it had alerted the Maltese and Italian authorities to launch a rescue immediately without delay as 90 people were in distress on a wooden boat in Malta's search and rescue area.
A source confirmed the bulk of the migrants had been transferred on to the merchant vessel Marina.
The migrants had requested to be taken to Lampedusa, and the vessel was awaiting instructions from Rome about how to proceed. It is currently stationed outside Lampedusa's territorial waters.
Meanwhile, a video sent to Times of Malta shows a group of migrants rescued on Saturday, waiting to be processed at the Lampedusa port. Many of those migrants had been left outside for 24 hours as Lampedusa struggled to keep up with the influx.
Maltese and Italian ports are currently closed due to the COVID-19 pandemic.
An official briefed on the situation said Malta's position had not changed. "The EU needs to wake up", the official said.
Alarm Phone raised alarm about the migrants' wooden boat early in the morning, saying it was out of fuel and drifting, with those on board, including a pregnant woman, desperate for rescue. Any delay in rescue, it said, would endanger their life.
It said at 7.30am that although two merchant vessels Marina and Pyxis Epsilon were monitoring the situation, there was no rescue in sight and a tragedy could happen at any moment.
By 8.15am, the organisation reported that it had lost contact with the boat but according to the last contact it had the situation was critical, especially for the elderly and one person who was unconscious.
It said that a third merchant vessel Karina was also on the scene.
"We fear another illegal pushback to Libya organised by Malta," Alarm Phone said.
Meanwhile, Mediterranea Saving Humans tweeted it was informed Malta has taken over the coordination of the case and asked three commercial ships to intervene.
It asked for the migrants not to be sent to Libya. "They must be rescued in a European port," it said.
Malta is currently holding 56 migrants rescued out at sea earlier this week on a Captain Morgan tourist boat outside territorial waters, a decision described as "bizarre" by Opposition leader Adrian Delia.
Prime Minister Robert Abela faced criticism in April over the decision to close Malta’s ports, with the Opposition insisting that vulnerable people like children and pregnant women should be rescued.
It has since been exposed how the government sanctioned an operation that saw private fishing vessels picking up migrants to ferry them back to Libya.
Former OPM official Neville Gafa' has claimed in court that he helped arrange the operation.
Abela has refuted accusations that the government pushed back the migrants, instead insisting it was a rescue mission.