Mohammed and the other accused conspirators have been held for years at the US-run prison in Guantanamo Bay, Cuba, amid a legal and political battle over how and where to prosecute them.
"The charges allege that the five accused are responsible for the planning and execution of the attacks of Sept. 11, 2001, in New York and Washington DC, and Shanksville, Pa., resulting in the killing of 2,976 people," the Defense Department said in a statement.
If convicted before a military tribunal, "the five accused could be sentenced to death," it said.
After more than 10 years since the attacks that jolted the American psyche, "it is important to see that justice is done," said White House spokesman Jay Carney.
He also said that President Barack Obama was still committed to making good on his promise to close the prison at Guantanamo, a pledge he had to back away from after legal setbacks and stiff opposition in Congress.
The 46-year-old Mohammed, along with Walid bin Attash of Saudi Arabia, Yemen's Ramzi Binalshibh, Pakistan's Ali Abd al-Aziz Ali -- also known as Ammar al-Baluchi -- and Mustapha Ahmed al-Hawsawi of Saudi Arabia, are due to appear in court for arraignment proceedings within 30 days, the Pentagon said.
The joint trial, which could be months away, will be held at the American naval base in Guantanamo Bay, where the US government has set up special military commissions to try terror suspects.
Mohammed, whom US officials refer to simply as "KSM," has been at the center of a years-long debate over the legal fate of the accused plotters.
After he was captured nine years ago, Mohammed was subject to harsh interrogations and repeated "waterboarding," a simulated drowning technique that has been widely condemned as torture.
His treatment has raised questions whether his statements to interrogators will hold up in a trial, but testimony from a former aide may resolve that problem.
His former deputy, Majid Khan, accepted a plea deal recently with US authorities that will require him to testify against the other suspects.
After taking office in 2009, Obama initially sought to try Mohammed and the four others in a civilian court in New York, not far from the Ground Zero site where the World Trade Center's twin towers fell in 2001.
But the proposal sparked criticism and Republicans in Congress put an end to those plans by blocking the transfer of terrorism suspects to the United States.
Human rights groups have slammed the Guantanamo tribunals as tainted and renewed demands Wednesday that terror suspects be tried in a federal courts by civilian judges.
"The Obama administration is making a terrible mistake by prosecuting the most important terrorism trials of our time in a second-tier system of justice," Anthony Romero, American Civil Liberties Union executive director, said in a statement.
A lawyer for one of the accused said his client, Ali of Pakistan, would not be facing execution if he was being tried in a civilian court.
"Because he did not kill or plan to kill, Mr. Ali would not be eligible for the death penalty if this case were tried in federal court," James Connell said in a statement.
The military tribunals were created under George W. Bush's presidency after the 9/11 attacks, with officials arguing that Al-Qaeda militants fell into a special category that did not suit civilian courts.
Procedures for the military tribunals, also known as commissions, have since been modified by the Obama administration to make them more closely resemble civilian courts.
Mohammed and the other accused plotters were charged once before under the Bush era and, now that the system has been revised, had to be formally charged again to clear the way for a trial.
The five are charged with terrorism, hijacking aircraft, conspiracy, murder in violation of the law of war, attacking civilians, attacking civilian objects, intentionally causing serious bodily injury, and destruction of property in violation of the law of war.
