In a statement, the FBI said the letter containing a granular substance that preliminarily tested positive for ricin was received at an offsite mail screening facility.
"The envelope, addressed to the President, was immediately quarantined by US Secret Service personnel, and a coordinated investigation with the FBI was initiated," it said.
This was the second letter - the other being sent to a Senator - which have been tested positive for ricin, federal investigating agencies said. Obama has been briefed on the matter, White House Press Secretary Jay Carney told reporters at his daily news conference.
Operations at the White House have not been affected as a result of the investigation, the statement said adding that filters at a second government mail screening facility preliminarily tested positive for ricin this morning. Mail from that facility is being tested. "There is no indication of a connection to the attack in Boston," the FBI said.
The Secret Service White House mail screening facility is a remote facility, not located near the White House complex, that all White House mail goes through. "The Secret Service is working closely with the US Capitol Police and the FBI in this investigation," the Secret Service said in an earlier statement.
The White House has been put under heightened security alert after Monday's bomb blast in Boston that killed three person and injured more than 170.
The security perimeter around the White House has been increased. "For a long time now there have been long-established procedures and protocols. Any time a suspicious powder is located in a mail facility, it is tested.
"And I would underscore that the mail sent here is screened and that these tests are undertaken at remote sites to mitigate the risk both to those recipients and to the general population," Carney said. A day earlier, Senator Carl Levin, Chairman of the Senate Armed Services Committee, said that he too received a suspicious letter at his Michigan office.
"The letter was not opened, and the staffer followed the proper protocols for the situation, including alerting the authorities, who are now investigating. We do not know yet if the mail presented a threat," Levin said in a statement.
A day earlier, an envelope addressed to a senior Republican Senator was tested positive for ricin, a poisonous substance, which added to the heightened concerns in the United States.
The Senate Majority Leader, Harry Reid, told reporters at the Capitol Hill that the letter was addressed to Senator Roger Wicker from Mississippi, which has tested positive for ricin. His security has been increased.
According to the Centers for Disease Control and Prevention, Ricin is a poison found in castor beans, which can be manufactured from castor bean waste materials. After the 2001 anthrax scar, all the mails sent to the lawmakers are screened at an off-site facility.