The boat was taking on water near the Tunisian island of Djerba when it was intercepted, the ministry said.
All 98 migrants on board were rescued. It was not immediately clear which countries they came from.
African migrants frequently try to reach Europe from Libya’s coast, and the southern Italian island of Lampedusa is just 113 km (70 miles) from the coastline of North African neighbour Tunisia.
In October, more than 300 people drowned or were feared dead after a boat packed with migrants sank off Lampedusa, one of the worst disasters in Europe’s struggle to cope with heavy immigration.
Libya’s security forces are not well equipped and are often unable to stop smugglers who have profited from the country’s chaos since the uprising that led to the death of its leader, Muammar Gaddafi, nearly three years ago.
