On Wednesday, grim work remained in accounting for the dozens still missing, including the driver at the centre of the investigation into the wreck.
An investigation into possible negligence by operator West Japan Railway Co or JR West has focused on the actions of the 23-year-old driver, his lack of experience and suspicions that the train was speeding before it derailed and slammed into an apartment building on Monday.
At least 456 people were injured.
Rescuers at the crash site in Amagasaki, about 410km west of Tokyo, found 13 bodies in the early hours of Wednesday, Hyogo prefecture (state) police said.
They also found a body seated at the front of the train and thought to be that of the driver Ryujiro Takami, but that had not been confirmed, the Kyodo news agency said.
The toll was expected to rise, with police saying an unknown number of victims were still in the wreckage.
JR West said 47 people had contacted them saying their relatives or friends might have been on the train and were unaccounted for.
"The driver had only 11 months of experience and we can only say that JR West's employee training and its tests to evaluate the suitability of drivers had problems"
Japanese transport minister
Rescue workers used power shovels to peel away the twisted metal of the two worst-damaged train cars, flattened against the apartment building.
Transportation Minister Kazuo Kitagawa indicated the government would order JR West to review the way it operates after it completes its investigation into the accident.
"The driver had only 11 months of experience and we can only say that JR West's employee training and its tests to evaluate the suitability of drivers had problems," Kitagawa said in parliament. "I would like to issue instructions to them based on the results of our investigation."
The authorities swarmed eight offices of JR West on Tuesday, carting away cardboard boxes of documents in their investigation into possible professional negligence.
Government investigators examining the accident site said they had found the train's black box, a computer chip that stores such information as the train's speed in the final seconds before an accident.
The train was said to be travelling
30kph above the speed limit
But they said the contents would take some time to analyse.
National broadcaster NHK reported that police suspected the train was going 100kph, above the 70kph speed limit, when it hit the curve where it derailed.
Investigators said the driver might have been shaken after overrunning the last station by 40m and falling 90 seconds behind schedule.
Workers freed two survivors from the wreckage early on Tuesday, but police said they did not expect to find anyone else alive.
The seven-car train was crowded with 580 passengers when it jumped the tracks near the Osaka suburb and plunged into the first floor of an apartment complex.
The driver got his train operator's licence in May last year.
Monday's accident was the worst
railway disaster since 1963
One month later, he overran a station and was issued a warning for his mistake, railway officials and police said.
Deadly train accidents are rare in Japan. Monday's accident was the worst railway disaster in nearly 42 years in the safety-conscious country which is home to one of the world's most complex, efficient and heavily travelled rail networks.
A three-train crash in November 1963 killed 161 people in Tsurumi, outside Tokyo.
Another accident killed 42 people in April 1991 in Shigaraki, western Japan.