The engine and all seven cars of Northeast Regional Train 188 derailed at about 9:30 p.m. near a sharp curve in a section of the corridor known as Frankford Junction. The train was carrying five crew members.
Five people were initially reported killed after the crash, and a sixth person died overnight at Temple University Hospital, officials said. As many as eight people were critically injured, officials said.
Philadelphia Mayor Michael Nutter said Wednesday officials have yet to match a manifest from Amtrak against lists of people admitted to hospitals. More than 200 people went to area hospitals, according to Samantha Phillips, director of Emergency Management for the city. Many have since been released.
One of the passengers who died was a midshipman at the U.S. Naval Academy, which is located in Annapolis, Md., according to a person familiar with the situation.
Mr. Nutter said a "black box" data recorder aboard the train had been recovered and is being analyzed at an Amtrak facility in Delaware. He said it was too soon to speculate on the cause of the accident.
"We are heartbroken at what has happened here," Mr. Nutter said at a news conference. "We have not experienced anything like this in modern times."
Robert Sumwalt, a member of the National Transportation Safety Board, the lead agency investigating the accident, said investigators would study a variety of factors, including the condition of the track, train signals, the mechanical condition of the train and human performance.
Mr. Nutter said the train's engineer, who wasn't identified, was treated after the accident and gave a statement to Philadelphia police.
President Barack Obama praised first responders for their handling of the derailment in a written statement Wednesday. "Michelle and I were shocked and deeply saddened to hear of the derailment," he said. "Our thoughts and prayers go out to the families and friends of those we lost last night, and to the many passengers who today begin their long road to recovery."
The train originated in Washington and was due in New York about 10:30 p.m. But shortly after leaving Philadelphia's 30th Street Station, the train began to jerk and rock, passengers said.
"I was holding on to the table for dear life, and because of force just got thrown to the other side of the car, head first into the window, and my shoulder hit the guy who was there," former Pennsylvania Rep. Patrick Murphy, a passenger on the train, told MSNBC. He was uninjured.
More than 120 firefighters and 200 police responded to the chaotic scene that included several badly mangled railcars, officials said.
One car was flipped nearly onto its roof, another was close to toppled, and three were on their sides, the Federal Railroad Administration said. The engine and two cars stayed upright.
Rescue workers used hydraulic tools to help some trapped passengers escape from the wreckage, Mr. Nutter said.
The cause of the crash wasn't immediately known. The Amtrak official declined to speculate on whether the train's speed contributed to the derailment but noted the tight curve in the area has a speed restriction of 55 miles an hour.
Train service was canceled Wednesday between Philadelphia and New York, but New Jersey Transit plans to honor Amtrak tickets between New York and Trenton, N.J., Amtrak said. Mayor Nutter said Tuesday night he expected service between Philadelphia and New York could be shut down for the rest of the week.
Modified Amtrak service is planned between Washington and Philadelphia, Harrisburg and Philadelphia, and New York and Boston.
Temple University Hospital, which has a trauma center, said it had received 54 patients from the crash. Hospital spokesman Jeremy Walter said, Wednesday morning that one passenger died overnight and 25 remained at the hospital, including eight in critical condition. The injuries included broken bones and other limb injuries, he said.
Many patients taken to hospitals with lacerations and bruises had been released by Wednesday morning. Of 26 people treated at Aria Health's Frankford hospital near the crash site, 21 people were released, a spokeswoman for Aria Health said Wednesday.
Two patients had been transferred to the University of Pennsylvania Hospital and three went to Aria Health's Torresdale hospital. At Torresdale, 24 of 30 people admitted directly to the hospital had been released, the spokeswoman said, while a total of nine people remained hospitalized Wednesday morning.
Many of the patients at the Frankford campus walked in on their own and had lacerations, she said. She didn't have details about the Torresdale patients.
Hahnemann University Hospital received two patients, and Einstein Medical Center Philadelphia said it received 10 patients.
The FRA said it was sending at least eight investigators to the scene, including acting Administrator Sarah Feinberg. The NTSB said it had a team on site Wednesday morning, and U.S. Transportation Secretary Anthony Fox said Transportation Department officials were heading to the scene.
The crash occurred in the Port Richmond section of the city, a mix of residential and industrial buildings along the Delaware River. Mr. Nutter said the accident resulted in a four-alarm response from area fire stations. He described the accident as a Level 3 mass-casualty incident based on the number of people involved.
The last crash of this magnitude along the heavily-traveled Northeast Corridor occurred in 1987 near Baltimore. Sixteen people were killed when a Conrail train ignored signals and collided with an Amtrak train. The accident sparked several safety reforms.