Local media in California reported that a key prosecution witness, Colonel John Ewers, had also served as a legal adviser to the marine general who approved charges against Chessani.
A total of eight marines were initially charged in 2006 over the case.
However, only one defendant, Frank Wuterich, still faces multiple charges of voluntary manslaughter.
Earlier this month Lieutenant Andrew Grayson, 27, was found not guilty of ordering photos of the dead civilians to be deleted from army computers.
Grayson, an intelligence officer, was not present when the Iraqis were killed.
Deadly incident
The civilians, many unarmed men, women and children, were killed after a roadside bombing left a US marine dead in Haditha, 260km west of Baghdad, in November 2005.
Following the incident, the marines said in a statement that 15 Iraqis had died in the bombing that killed the soldier.
However, investigators say Wuterich and a squad member shot five men in a car after the bombing.
Wuterich, whose trial is set to take place later this year, then allegedly ordered his squad into several houses, where they attacked with grenades and gunfire, killing unarmed civilians.
The killings in Haditha are the most serious allegations of war
crimes involving US forces since the US-led invasion of Iraq in 2003.