"Our air force carried out a raid on terrorist elements who were planning attacks on vital installations (and) two Al-Qaeda leaders were killed," said a statement on the defence ministry's website.
It did not specify what installations were being targeted, but said that the air strike happened in Moudia region -- around 300 miles (480 kilometres) southeast of Sanaa -- which is close to the oil-rich province of Shabwa.
Yemeni authorities have intensified their campaign against the country's Al-Qaeda branch after it claimed a botched Christmas Day bid to blow up a US passenger plane over Detroit.
Earlier this month, a security official said 11 men were arrested in the capital Sanaa on suspicion of plotting attacks for Al-Qaeda.
Al-Qaeda militants have previously targeted Western embassies in the city.
Security forces arrested three suspected members of Al-Qaeda on February 17 in Marib province, east of the capital and on January 16 the authorities announced the arrest of three other suspected Qaeda militants.