Agents were in a race against time to find evidence of the al Qaida official's U.S. contacts before the capture became generally known.
Other evidence was packed up and sent to the United States for analysis at the FBI Laboratory.
Mohammed is believed to be the operational planner behind the Sept. 11, 2001, terror attacks in the United States, and a top lieutenant to Osama bin Laden, head of the al Qaida organization.
Agents hoped to be able to quickly connect Mohammed back to contacts within the United States and elsewhere, and possibly to learn the whereabouts of bin Laden and other leaders.
Although the FBI is not saying so publicly, the bureau would have preferred that news of Mohammed's arrest not be immediately publicized.
Pakistani officials announced the capture over the weekend.
Asked Monday whether the United States formally asked Pakistan to delay announcement of the capture until the FBI could fully exploit the clues taken with him, Assistant Attorney General Michael Chertoff said: "I won't get into that."
Chertoff, chief of the Justice Department's criminal division, also declined to say how the reward of up to $25 million for Mohammed's capture would be distributed.
Meanwhile, the U.S. official confirmed on background that the FBI got somewhat of a jump on looking at the evidence.
"There was some initial analysis done" on items in the Rawalpindi house where Mohammed was staying, the official said. "They (FBI agents already in Pakistan) did move fast over the weekend."
Mohammed was apparently captured very early Saturday while asleep in a house owned by Pakistanis in Rawalpindi, near the capital of Islamabad.
His picture was taken shortly after the capture, and his disheveled features have been published and broadcast around the world.
Among the items believed to have been confiscated after Mohammed's capture were a personal computer, laptop computers, paper documents and whatever detritus was found in his pockets.
FBI analysts are capable of recovering whatever information is available on the computers, even if it has been erased from the hard drives.
Mohammed's whereabouts at the present are uncertain and it is unclear exactly whose custody he is being held in.
The alleged al Qaida leader was on the FBI's list of 22 Most Wanted Terrorists. Similar to bin Laden, there was a reward of up to $25 million for his capture.
Besides being suspected in the September attacks, Mohammed is wanted in the United States for his alleged involvement in a Manila-based conspiracy to blow up commercial U.S. airliners flying to this country from Southeast Asia in January 1995. He was indicted for the alleged conspiracy in January 1996 in New York.
Others on the Most Wanted Terrorists list include bin Laden and his chief lieutenant, Ayman al-Zawahiri.
Besides the Sept. 11 attacks, bin Laden is suspected in the bombing of two U.S. embassies in East Africa in 1998 that killed more than 200 people. Al-Zawahiri is founder of the Egyptian Islamic Jihad and is also wanted in connection with the bombings.