Texas resident Kurt Mix, a former BP engineer, was arrested for allegedly destroying evidence and was charged with two counts of obstruction of justice.
The Deepwater Horizon oil rig exploded in April 2010, killing 11 men on board and pouring 200 million gallons of oil. It was the largest environmental disaster in U.S. history.
Authorities say Mix has been charged with deleting some 200 text messages with a BP supervisor in October 2010 that involved internal BP information about how efforts to cap the oil well were failing.
According to the Justice Department, Mix had been repeatedly notified that he needed to retain such information regarding the oil well.
The charges confirm what government scientists later established through video - BP was lying about the amount of oil coming out of the well.
BP said it was cooperating with the federal investigation.
"BP had clear policies requiring preservation of evidence in this case and has undertaken substantial and ongoing efforts to preserve evidence," the company said in a statement.
If convicted, Mix faces 20 years in prison and a fine of up to $250,000 for each count.