Almasdar Online said its sources said a number of other government soldiers were captured during the raids on posts in southern Yemen's Abyan province, the Yemen Post reported. It wasn't clear how many militants died in the fighting.
The news Web site said its sources said the attacks were in response to the killing of Fahd al-Quso in a drone attack a day earlier.
Al-Quso, 37, was a senior al-Qaida militant on the FBI's Most Wanted Terrorists list for the 2000 bombing of the USS Cole warship. He was hit by a missile while in or leaving a vehicle in the south-central Shabwa province, Yemeni military officials said.
Another al-Qaida operative was killed in the Sunday drone attack, officials told The New York Times and CNN.
Al-Quso had been the subject of a U.S. and Interpol international manhunt since 2003, after a New York federal grand jury indicted him on 50 counts of terrorism in the Oct. 12, 2000, bombing of the USS Cole while it was docked in the Yemen port of Aden.
Seventeen U.S. sailors were killed in the suicide attack and 39 were injured.
The indictment charged al-Quso with murder, conspiracy to kill U.S. nationals, attempted murder, conspiracy to use weapons of mass destruction against U.S. nationals, conspiracy to destroy U.S. buildings and property, damaging and destroying the USS Cole, and providing material support to a foreign terrorist organization alone and in conspiracy with others.
Al-Quso had been ordered to tape the bombing from an apartment on a hill above the port and to use the tape to recruit terrorists -- but he overslept and never made the tape, the National Commission on Terrorist Attacks Upon the United States, also known as the 9/11 Commission, said in a 2004 report.
Osama bin Laden allegedly funded the USS Cole attack.
The FBI had offered a $5 million reward for information leading to al-Quso's capture after he escaped from a jail in Yemen in 2003, where he had been held on suspicion of involvement in the USS Cole bombing.
The attack was the deadliest assault against a U.S. naval vessel since the frigate USS Stark was attacked by an Iraqi jet fighter during the Iran-Iraq War May 17, 1987. Thirty-seven Navy personnel were killed and 21 others were wounded in that missile attack.
The USS Cole was redeployed overseas Nov. 29, 2003, and returned to Norfolk, Va., May 27, 2004, without incident.