As the toll rose to 73, criticism of the government's recent rail privatisation grew.
In light rain that fell at the break of dawn on Tuesday, rescue teams squeezed into flattened carriages, pulling out the survivors and bodies. Cranes carefully removed train debris wrapped around an apartment building.
"The possibility of finding more survivors is getting lower now, but we will continue our operation as long as there is a possibility," said a fire department spokesman in Amagasaki, a western industrial and commuter town.
Police on Tuesday searched the Osaka headquarters of the West Japan Railway Co (JR West) as part of its probe into the accident, as outraged families asked how such an accident could happen in safety-conscious Japan.
"I am furious at JR West," Hirokazu Kobata, 57, said after seeing the body of his wife, Sachiko, 53.
"Please bring her back," Kobata said full of emotion at a gymnasium which has turned into a makeshift mortuary for bodies that were often too mutilated for identification.
The Yomiuri Shimbun newspaper questioned whether profit incentives at JR West, which was fully privatised last year, led to lax safety standards such as reducing labour costs.
Train driver Ryujiro Takami, 23, had 11 months experience at the job and had previously received warnings, including one time from passengers who complained he looked inattentive at the job, according to JR West officials.
Four of the train's carriages were
thrown from the tracks
Takami was believed to still be under the debris and it was unclear if he was dead or alive, a JR West spokesman said.
Four of the train's seven carriages were thrown from the tracks at a curve in Amagasaki, 410km west of Tokyo during the rush hour as workers and children began their Monday morning.
One carriage was completely bent across an apartment building with rubble piling up to the third floor.
Fear of explosion
"We are having difficulties due to fears of a possible explosion as the train destroyed several cars in the parking space on the first floor of the building and some gas leaked from the cars," a fire department spokesman said.
A 19-year-old university student was rescued 22 hours after the accident.
The student, wrapped with a blanket and transferred to hospital on a yellow stretcher, was in serious condition, but was able to identify himself as Hiroki Hayashi, the fire department spokesman said.
Two others were also rescued earlier in the day. An 18-year-old man was in serious condition while a 46-year-old woman had only injured her legs. Both were receiving treatment in hospital.
The accident put paid to the myth that Japan's train system was invincible.
World's safest railway
Japan has one of the world's most extensive and safest train networks, transporting about 60 million people - or nearly half the nation's population - each day.
It was Japan's worst accident since November 1963 when 161 people died in Yokohama near Tokyo when a freight train collided with a truck and was then hit by two passenger trains from opposite directions.
The crash is Japan's worst
accident since November 1963
"Why did this tragedy happen?" asked the influential Asahi Shimbun in an editorial.
"Japanese train systems are known for their punctuality and safety. The world is paying attention to this accident. We have no choice but to do all we can to analyse this from all angles," it said.