The campaigners used a motorised dinghy to approach the ship, which is travelling towrds the Suez canal in international waters off the Egyptian coast, the French ministry of defence said.
"We let them board. In no way are they impeding the Clemenceau's journey," said a spokesman.
The Clemenceau, which took part in the 1991 Gulf War, was taken out of service in 1997 when it was superseded by France's new, nuclear-powered aircraft carrier, the Charles de Gaulle.
It left the Mediterranean port of Toulon on December 31 after a long legal battle, and is due in India at the end of February.