The investigation included two planes at Philadelphia International Airport. Officials tell Action News that a total of six packages were removed from the planes there.
A total of 13 packages have been recovered in this entire operation, federal law enforcement sources said.
A federal law enforcement official, who was not authorized to provide information on the investigation, told the AP that nothing suspicious was found on them.
One of the planes is UPS #218 originating from Paris. The second plane is UPS #204 originating from Philadelphia.
Yemen is home to the al-Qaida branch that tried to bomb a U.S.-bound airliner on Christmas. No explosives have been found.
Intelligence and law enforcement officials discovered suspicious packages in the United Kingdom and Dubai late Thursday night, prompting national security officials to alert President Barack Obama to a "potential terrorist threat," the White House said.
RELATED: See pictures of the suspicious device from CNN
The UK package, discovered aboard a plane in East Midlands, about two hours north of London, contained a toner cartridge with wires and powder. It was found during routine screening of cargo in the United Kingdom, prompting authorities to scour three planes and a truck in the United States on Friday, U.S. officials said.
The two packages were addressed to Chicago religious sites, Chicago FBI spokesman Ross Rise said. One was a synagogue, said a U.S. official who spoke on condition of anonymity to discuss the ongoing investigation.
"The president directed U.S. intelligence and law enforcement agencies, and the Department of Homeland Security, to take steps to ensure the safety and security of the American people, and to determine whether these threats are a part of any additional terrorist plotting," the White House said in a statement.
Yemeni officials said they launched a terrorism investigation and Scotland Yard said its investigators were testing a number of items seized from the plane in East Midlands.
Searches also were conducted in Newark, N.J., and New York City. The packages were being sent via UPS.
A source with knowledge of the situation in Newark who was not authorized to speak publicly said the FBI and a bomb squad checked two packages there and gave the "all clear."
New York Police Commissioner Ray Kelly said that the NYPD removed a package from a UPS truck in Brooklyn, tested it for possible explosives and found it not to be dangerous. The package was an envelope that came from Yemen, appeared to contain bank receipts, and was addressed to the JP Morgan Chase bank in Brooklyn, Kelly said. The package arrived on a plane that landed at Kennedy Airport, he said.
Mike Mangeot, a spokesman for Atlanta-based United Parcel Service Inc., said two planes in Philadelphia that had come from Cologne, Germany, and Paris were being investigated.
"Out of an abundance of caution, those aircraft have been isolated, and they are looking into the shipments in question there," he said.
A third plane had arrived in Newark, N.J., from East Midlands airport in England. That plane was cleared and flew to UPS' main hub in Louisville, Ky., on its usual route, Mangeot said.
In central England, police had evacuated a freight distribution building at East Midlands Airport after a suspicious package was reported at 3:30 a.m. Police and emergency workers examined the package and lifted the security cordon by midmorning, but Leicestershire Constabulary later said officers were re-examining it "as a precaution."
All inbound and outbound flights into Philadelphia are continuing at this hour.
To check the status of your flight, call 1-800-PHL-GATE or follow this link to the 6abc.com Flight Tracker.
The Associated Press contributed to this report.
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RELATED: More coverage from ABC station WABC in New York.
RELATED: More coverage from ABC station WLS in Chicago.
