Two other Marines also have been charged, their attorneys said Thursday.
In all, eight Marines could face charges in the biggest U.S. criminal case involving killings to arise from the war in Iraq.
Staff Sgt. Frank D. Wuterich, the squad leader, was charged with fatally shooting 12 people while having "intent to kill or cause great bodily harm," according to charging sheets released by defense attorney Neal Puckett. Wuterich also was accused of telling Marines "to 'shoot first and ask questions later' or words to that effect," the charging sheet stated.
Wuterich, of Meriden, Connecticut, also was charged with soliciting a corporal to make false statements and making another staff sergeant make a false official statement.
Puckett said his client is not guilty and acted lawfully.
Lance Cpl. Justin Sharratt of Carbondale, Pennsylvania, was accused of one charge of murder involving unpremeditated killings of three males in a house, said his attorney, Gary Myers.
"Our view has been and continues to be that these are combat-related deaths,"Myers said.
Lance Cpl. Stephen Tatum of Edmund, Oklahoma, also was charged, but his attorney, Jack Zimmerman, declined to specify the allegations before the government's announcement.
The Marines all belonged to Kilo Company of the Camp Pendleton-based 3rd Battalion, 1st Marines Regiment, and have been under investigation since March for the deaths.
Defense attorneys have said their clients were doing what they had been trained to do: responding to a perceived threat with legitimate force. The Marines remained in combat for months after the killings.