Tolbert says there's no indication that this summer's track fix work at the nation's busiest rail station played a part in the delay.
A NJ Transit train also derailed at Penn Station on July 6.
Amtrak officials said the trains stopped because there were electrical issues with power in the overhead wires.
It happened just before 5 p.m. between the platform and the tunnel.
A New Jersey Transit and Amtrak train, carrying close to 1,000 people between them, got stuck in a Penn Station tunnel earlier Saturday, officials said.
When the first rescue train couldn't reach the stalled train, a second locomotive was sent in and towed everyone to safety after about two hours.More news: ATM Spits Out Desperate Note From Trapped Man
Amtrak travel between NY and New Jersey was briefly suspended, but had resumed on Amtrak rails by 1:15 p.m.
The Port Authority of NY and New Jersey said its PATH trains from Hoboken and Jersey City, New Jersey, cross-honored an average of about 23,000 NJ Transit fares on the first four days.
The train with about 600 passengers was delayed right before entering Penn Station at 4:45 p.m.
MTA chairman Joseph Lhota said Friday transit officials have "been able to keep things moving across the system" after the first week of Amtrak's summer-long project to fix and replace tracks and signals. No work crew injuries were reported this week, he said.
The project began on Monday and is expected to continue through September, although commuters said the first week of the project went mostly smoothly.