The judge, Maj. Brian E. Kasprzyk, admonished the courtroom, telling them: "There will be no more of that."
The verdict came just five hours after deliberations began.
Grayson, who has always maintained he did nothing wrong, was not present at the scene of the killings on Nov. 19, 2005, in Haditha. He was accused of telling a sergeant to delete photographs of the dead from a digital camera and laptop computer.
Grayson was found not guilty of two counts of making false official statements, two counts of trying to fraudulently separate from service, and one count of attempt to deceive by making false statements.