A major civil trial set to take place in New Orleans has been delayed until February 2013.
Transocean, the owner and operator of the rig, also has unresolved liability issues. The DOJ, in its September filing, said the company is also guilty of gross negligence.
"BP did not act alone, by any means, and its gross negligence and willful misconduct are inextricably joined with the acts and omissions of Transocean," the government said in the filing.
Without naming Transocean, BP said Thursday it is not the only company to blame for the accident.
"Today's agreement is consistent with BP's position in the ongoing civil litigation that this was an accident resulting from multiple causes, involving multiple parties, as found by other official investigations," said the company's statement.
BP will have up to six years to pay the money it agreed to as part of the settlement. Most of that money -- $2.4 billion -- will go to the National Fish & Wildlife Foundation, an independent not-for-profit conservation group chartered by Congress in 1984. It is a windfall for the group, whose total contributions and commitments since its founding are just above $2 billion.
Another $350 million will go to the National Academy of Science.
BP identified the remaining $1.256 billion of the settlement as a "criminal fine." More than $1 billion of that fine will go to the U.S. Coast Guard's Oil Spill Liability Trust Fund, to be available for cleanup -- and compensation for those affected by -- oil spills in the Gulf .
It is single largest criminal fine on record. The previous record was $1.195 billion criminal fine paid by Pfizer as part of a $2.3 billion settlement in September 2009 over the fraudulent marketing of anti-inflammatory arthritis drug Bextra.
--CNNMoney's Mark Thompson and CNN's David Ariosto contributed reporting to this article.