While the charges against Mr Mix do not relate to who was ultimately to blame for the spill, the amount of oil that gushed into Gulf waters is central in determining the size of fine that BP is likely to face.
The Department of Justice is “continuing its investigation into the explosion”, Eric Holder, the US attorney general, said.
The explosion, whose second anniversary passed last week, killed 11 people and spewed millions of barrels of oil into the Gulf.
Mr Mix ignored requests from BP to preserve all evidence relating to the spill, prosecutors alleged. The engineer could face up to 20 years in prison and a fine of $250,000 (£155,000) if found guilty.
According to Bloomberg, Mr Mix did not enter a plea at a federal court hearing in Houston yesterday.
BP said it had a clear policy on the need to preserve evidence but declined to comment further.
The oil major last week finalised its $7.8bn settlement with the victims of the Gulf of Mexico oil spill in a move that significantly reduces the chance of a trial.