Thirteen carriages of the Gyaneshwari Express travelling from Kolkata to Mumbai jumped the tracks and most of the casualties were in four that collided with an oncoming goods train.
More than 200 people were injured, some of them critically.
The train derailed in the Jhargram area of West Bengal state's Midnapore district, known to be a stronghold of Maoist rebels.
More than 30 hours after the incident, emergency teams were still trying to cut their way into crushed compartments.
"So far, 90 bodies have been recovered," Surajit Kar Purakayastha, the police inspector in West Bengal, said.
"But that's going to rise as two of the carriages that crashed into the freight train are yet to be fully searched."
Srikumar Mukherjee, West Bengal's civil defence minister, said as many as 70 passengers were still missing.
The Indian Railways Board responded by cancelling night-time services in a number of Maoist-affected areas until further notice.
The precise cause of the derailment is still unclear.
However, Mamata Banerjee, the federal railways minister, said Maoists had blown up the track with explosives, while police pointed to evidence that a section of rail had been manually removed.
The Maoist rebels had called for a four-day strike in the area starting on Friday.
Senior police officials have laid the blame squarely at their feet, citing several leaflets that had been left at the site of the railway disaster.
Act of sabotage
Bhupinder Singh, the police chief in West Bengal, said that a Maoist group, the People's Committee Against Police Atrocities (PCPA), had claimed responsibility for the act of sabotage.
"We have recovered two posters by a local Maoist militia from the site of the accident," he said.
"They have claimed responsibility for the incident in the posters. It is a clear case of sabotage. The Maoists have done it."
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Al Jazeera's Prerna Suri, reporting from New Delhi, said no official confirmation has come from the federal government which "still maintains it was sabotage".
"However, these attacks follow a similar pattern but we will have to wait and see how seriously these links are being taken by the government," she said.
Less than two weeks ago, Maoist rebels ambushed a bus in central India, killing 31 police officers and civilians.
A few weeks before that, 76 soldiers were killed in a suspected Maoist ambush.
Buddhadeb Bhattacharya, the chief minister of West Bengal, said the latest attack warranted a further review of the government's counter-insurgency strategy.
"We have to find ways to counter the Maoist menace. Innocent people are being killed," he said.
Series of attacks
Maoist fighters in the eastern region have been blamed for a series of attacks on police, government buildings and infrastructure such as railway stations.
In recent months they have stepped up attacks in response to a government security offensive to clear them out of their jungle bases.
The uprising by Maoists, also known as Naxals, began in West Bengal in 1967 in the name of defending the rights of tribal groups, and has since spread to 20 of India's 28 states.
Manmohan Singh, India's prime minister, has described the uprising as India's biggest internal security challenge.