At least 17 migrants are missing after a night-time rescue of more than 100 others from a partially submerged rubber boat off the coast of Libya, the Migrant Offshore Aid Station (MOAS) said on Thursday.

Italy's coastguard received a distress call from the vessel on Wednesday evening and alerted the privately funded MOAS ship Phoenix, which used remote-controlled drones to locate the boat, a statement said.

The Phoenix crew pulled 113 to safety, but survivors said it had set out from Libya with 130 on board. Among those missing was a Nigerian toddler who was about to turn 3 years old, his mother told rescuers.

"The sea was rough and the boat was taking on water. At one point some people started to panic. The next thing I knew I was pushed into the water and I lost my son in the chaos," the boy's mother told the Phoenix crew, MOAS said.

A young man said five of his friends were missing, and another man said a 16-year-old girl also had disappeared.

Photographs posted on the MOAS web site show that many migrants were in the water and clinging to the boat when rescuers arrived. A search for the bodies had to be abandoned due to rough seas, the statement said.

Many of those rescued suffered burns caused by leaking fuel, and one woman was in shock with first-degree burns on a third of her body, MOAS said. A medical evacuation for her had been blocked by bad weather.

Separately on Wednesday, two rescue vessels operated by MOAS and Save the Children rescued a total of 470 migrants, an Italian coastguard spokesman said.

The central Mediterranean route between North Africa and Italy is the deadliest border in the world for migrants. More than 3,100 have gone missing or died this year while trying to use this route to reach Europe by boat, the International Organization for Migration estimates.