Lieutenant Andrew Grayson, 27, was declared "not guilty on all charges" by a jury, said a spokesman for Camp Pendleton, the military base 130 kilomters (80 miles) south of Los Angeles where the court martial began on May 28.
Grayson had been charged with obstruction of justice, making false statements and attempting to fraudulently separate from the Marine Corps.
He was the first to go on trial of eight soldiers and officers initially charged with crimes in connection with the November 2005 incident, which saw men, women and children shot dead by Marines in the aftermath of a roadside bombing.
Four soldiers faced murder charges and four officers, including Grayson, were accused of covering up and failing to properly investigate the killings.
However, since charges were first announced in December 2006, prosecutors have struggled to make the allegations stick.
Six of the eight men have now had charges against them dropped, while charges of murder were replaced by the lesser offense of manslaughter in the case of squad leader Frank Wuterich, who faces trial later this year, along with Colonel Jeffrey Chessani.
The killings in Haditha are the most serious war crime allegations leveled at US forces since the 2003 invasion to topple Saddam Hussein.
© 2008 Agence France Presse