The explosion and fire ripped through two of the cars of the train around midnight local time, although officials said the toll could have been much higher. Two unexploded suitcase bombs were reportedly found in undamaged parts of the train. Inside one, an electronic timer was packed next to more than a dozen plastic bottles containing a cocktail of fuel oils and chemicals.
An Indian Home Ministry official, speaking to the Associated Press on condition of anonymity because of the ongoing investigation, said no suspects had been ruled out -- from Kashmiri separatists to Hindu extremists.
Those who survived reported that the fire swept through the train, catching many travelers sleeping and trapping scores of screaming victims.
"We were sleeping after having dinner," one woman told Reuters. "When we woke up there was fire. Everyone was crying 'please save us, please save us, please stop the train!'."
Another survivor told how panicked passengers sought any escape from the flames.
"It was a huge fire. People were shouting for help. That caused panic in other carriages and people in those carriages also started shouting," Eighty-year-old Noor Mohammad said.
Witnesses first on the scene described an inferno.
"The coaches were totally engulfed in flames. I brought out three charred women - I could only recognize them as women because they were wearing bangles," Shiv Ram, a police railway constable, told the BBC.
Bodies were laid out in blue bags between huge slabs of melting ice in a morgue in the nearby northern town of Panipat. Officials said about 30 of the bodies were charred beyond recognition.
In the Indian capital of New Delhi, Prime Minister Manmohan Singh issued a statement condemning the attack and pledging to bring those who planted the bombs to justice.
"The Prime Minister expressed anguish and grief at the loss of lives. The culprits will be caught," a spokesman for the prime minister said.
Pakistani Foreign Minister Khurshid Kasuri reacted with both shock and outrage over the attack.
"Innocent men and women lost their lives (and) most of the dead are Pakistani," he said. "We would like (the) Indian government to investigate this incident and we are waiting for the results."
Despite his call for an Indian investigation, Kasuri also indicated he would continue with a planned trip to India to continue negotiations between the two nuclear rivals.
The foreign minister was due to sign a new agreement aimed at reducing the risk of nuclear accidents on Wednesday and there was no word if the deadly attack would impact those plans.
In Islamabad, Pakistani President Pervez Musharraf said the two nations would not let this act of "terrorism" derail continued talks.
"We will not allow elements which want to sabotage the ongoing peace process and succeed in their nefarious designs," Musharraf was quoted as saying by state-run Associated Press of Pakistan.
The train service between the two nations, begun again in 2004, was one of the most visible signs of rapprochement between the two nations.
Monday's blaze revived memories of earlier train attacks, including a series of bombings in July 2006 that killed more than 200 people in Mumbai. Indian Police blamed those attacks on Lashkar-e-Tayyaba, a Pakistan-based Islamic militant group, as well as the Students' Islamic Movement of India, a banned Indian group.
Indian Officials also alleged Pakistani intelligence was involved, a claim Pakistan denied.