The soldiers were carrying out "dangerous intelligence operations", according to French President François Hollande.
"It's only a few hundred kilometres from Europe's shores. And at the moment we're carrying out dangerous intelligence operations," he said. "Three of our soldiers who were, in fact, involved in these operations have lost their lives in a helicopter accident."
"Defence Minister Jean-Yves Le Drian regrets the loss of three French officers who died while on mission in Libya," a ministry statement said without giving any details on the circumstances of their deaths.
Le Drian praised the "courage and devotion" of the slain soldiers and sent his condolences to their families.
Earlier an Islamist militia had claimed that two French soldiers had been killed when it shot down a helicopter carrying them near Benghazi.
Earlier government spokesman Stéphane Le Foll confirmed that French special forces are active in Libya.
Previously the government has only admitted that its warplanes carry out reconnaissance flights over the country and refused to confirm reports by Le Monde newspaper that special forces were present.
Le Foll also said that Defence Minister Jean-Yves Le Drian, who is in Washington for a meeting of countries fighting IS in Iraq and Syria, was "preparing with the Americans a coordinated attack by coalition forces on Mosul", the key Iraqi city held by the fundamentalist organisation.