The change came Tuesday after both agencies recommended pausing use of the J&J COVID-19 vaccine.
Federal officials announced the discovery of severe blood clots in six woman who received the shot two weeks ago. One woman died and another is in critical condition.
None were from the Philadelphia area.
Philadelphia officials were originally planning on switching to the Johnson & Johnson Wednesday at the FEMA-run site at the Pennsylvania Convention Center in Center City, but now they're mainly relying on current supply of the Pfizer vaccine.
"We've had more Pfizer coming into the city than we've been able to administer each week. Pfizer is the one that needs ultra cold storage, and so it's the most difficult to use. There is Pfizer in storage in various places, some in the health department, some in other hospitals around the city," said Philadelphia Health Commissioner Dr. Thomas Farley.
Farley said they're confident they'll be able to maintain the 6,000 appointments a day at the Convention Center by administering the Pfizer vaccine.
"Johnson & Johnson was a pretty small fraction of the total doses for delivery. As you know, we were already dealing with a shortage of the Johnson & Johnson vaccine. Fortunately we have these other two that are excellent vaccines and fortunately, there's some level of protection, even with that first dose," Farley said.
All of Philadelphia's suburban counties have also stopped administering the Johnson & Johnson vaccine as recommended by the nation's top health agencies.
SEE ALSO: Philadelphia area pauses use of Johnson & Johnson COVID-19 vaccine
Chester County clinics have made the switch. Delaware County officials said they are requesting a larger shipment of Moderna and Pfizer.
Some clinics in Montgomery and Bucks counties will remain closed Wednesday but appointments are being rescheduled.
"We're waiting to see if there is some of connection with the vaccine or if there's some kind of coincidence," said Bucks County commissioner Bob Harvie.
Most counties in the region are requesting additional doses to fulfill appointments that are already scheduled on top of covering people who will later become eligible.