A statement said only that he died "along with some of his companions".
Awlaki, of Yemeni descent, was on the run in Yemen since December 2007.
The US has named him a "specially designated global terrorist" for his alleged role in a number of attacks and US President Barack Obama is said to have personally ordered his killing.
The defence ministry gave no further details of his death, which could not be independently verified.
But tribal sources told AFP news agency Awlaki was killed in an air strike in the eastern Marib province, said to be an al-Qaeda stronghold.
It is not clear whether he was killed by Yemeni forces or a US drone strike.
BBC security correspondent Gordon Correra says the killing, if confirmed, is significant, because Awlaki is able to reach out to people susceptible to radicalisation through his use of the media.
He is described by US officials as a key leader of al-Qaeda in the Arabian Peninsula.
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Al-Qaeda in the Arabian Peninsula
* Formed in January 2009 by a merger between al-Qaeda in Saudi Arabia and Yemen
* Based in eastern Yemen
* Led by Nasser al-Wuhayshi, a Yemeni former aide to Osama Bin Laden. Deputy leader is Saudi ex-Guantanamo inmate Said al-Shihri
* Aims to topple Saudi monarchy and Yemeni government, and establish an Islamic caliphate
* Came to prominence with Riyadh bombings in 2003, and 2008 attack on US embassy in Sanaa
* Says it was behind an attempt to blow up US passenger jet in December 2009
He has been implicated in the US army base killings in Fort Hood, Texas, the Christmas 2009 Detroit airline bomb attempt, and a failed bombing in New York's Times Square.
When he was imam of a San Diego mosque in the 1990s, his sermons were attended by two future 9/11 hijackers, Khalid al-Midhar and Nawaf al-Hazmi.
In a video posted in November last year he called for the killing of Americans, saying they were from the "party of devils".
Weeks later, he survived an air strike in Shabwa province in which at least 30 militants were killed.
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