Two children are dead and a person is missing after a migrant boat in distress capsized in the southern Mediterranean as a merchant ship tried to save the people on board, Sea Watch said on Wednesday.

The search-and-rescue NGO said the survivors are currently on board the ship and risk being taken back to North Africa by the Libyan coast guard, saying they face "torture and death" there.

"We had seen the boat in trouble with 90 people on board at sea for three days," it said.

"We called for help.

Frontex arrived 6 hours later, saw the boat and left.