President Barack Obama called the coordinated attacks a "credible terrorist threat," and U.S. officials said they were increasingly confident that al-Qaida's Yemen branch, the group responsible for the failed Detroit airliner bombing last Christmas, was responsible.
He said the packages, found in the UK and Dubai on two overnight cargo planes from Yemen, were destined for Jewish places of worship in Chicago.
Security alerts are under way in the US, UK and Middle East.
The White House later said Saudi Arabia had provided information that helped identify the threat.
The two packages found in Britain's East Midlands airport and in Dubai have now been made inert, US officials say.
UK Home Secretary Theresa May later said that the device found in Britain "did contain explosive material".
"But it is not yet clear that it was a viable explosive device. The forensic work continues," she added.
The security alert saw two other cargo planes owned by the freight company UPS searched in Newark and Philadelphia.
UPS said it had suspended its shipments out of Yemen.
Another suspect package from Yemen was examined on a delivery lorry in New York, and later declared safe.
In other developments:
- New aviation security measures are being taken in light of the alert,the US Homeland Security Department announces
- The US says that if a terror link is confirmed, the main suspects will be al-Qaeda's branch in Yemen - al-Qaeda in the Arabian Peninsula (AQAP)
- US fighter jets escorted Emirates flight 201 from Dubai into New York, with officials saying the action was being taken "out of an abundance of caution" because cargo from Yemen was on board
- Cobra, the UK government's emergency planning committee, met on Friday and was to meet again on Saturday as discussions continue about how to tighten UK security further
Mr Obama said the discovery represented a credible terrorist threat against the US.
"Although we are still pursuing all the facts, we do know that the packages originated in Yemen," he told a White House press conference.
"We also know that al-Qaeda in the Arabian Peninsula - a terrorist group based in Yemen - continues to plan attacks against our homeland, our citizens and our friends and allies."
Mr Obama said he was first informed about the packages late on Thursday and that President Ali Abdallah Saleh of Yemen had pledged his country's full support in investigating the threat.
However, the Yemeni government later expressed astonishment at reports linking the country to the two packages, according to the Associated Press news agency.
It quoted a Yemeni statement as saying that no UPS cargo planes had taken off from Yemen and there had been no direct or indirect flights to British or US airports.
Mr Obama said the US would continue to work to destroy al-Qaeda and its affiliates, and to root out violent extremism in all its forms.
US Homeland Security adviser John Brennan thanked the Saudi Arabians for their help.
"Their assistance, along with the hard work of the US counter-terrorism community, the United Kingdom, the UAE, and other friends and partners helped make it possible to increase our vigilance and identify the suspicious packages," he said.
A spokeswoman for the Jewish Federation in Chicago said the community had been warned to be on the alert in the wake of the discoveries.
"We were notified this morning that synagogues should be on the alert," the spokeswoman, Linda Haase, told Reuters news agency. "We are taking appropriate precautions and are advising local synagogues to do likewise."
The suspicious package in the UK was reportedly an ink toner cartridge that had been modified.
US officials told Associated Press they believed the Dubai and East Midlands packages contained the same explosive used in the failed bombing of a US-bound airliner last Christmas Day.
It quoted the officials as saying that full testing had not been completed but initial indications were that the packages contained PETN, a chemical that was also a component of shoe bomber Richard Reid's explosive in 2001.
The cargo planes in the US were taken to remote locations to be searched.
"Out of an abundance of caution the planes were moved to a remote location where they are being met by law enforcement officials," said the Transportation Security Administration.
Emergency services were called to the UK airport in Donington, Leicestershire, overnight and evacuated a distribution centre, while the suspicious package was examined.
US security services remain on a high level of vigilance in the wake of the attempted Times Square bombing in May and the alleged attempted Christmas Day attack.