The Jaffar Express, carrying some 400 passengers in nine coaches, was going from Quetta to Peshawar when militants derailed it using explosives and hijacked it.
They added that the number of the passengers, who were killed at the beginning of the attack, was being determined.
Sources said that several terrorists present at the scene have been killed, adding that more details will be available soon.
A Pakistan minister refused to give any timeline for the conclusion of the ongoing operation against the militants but vowed to complete it at the earliest.
He also warned against the fake news, saying no mobile internet network was working in the area and all video clips being circulated on the media in Pakistan and elsewhere were fake.
He said that the passengers included civilians, government employees and security personnel.
Balochistan government spokesman Shahid Rind said the operation would continue until all passengers were rescued.
Rind said extra care was being taken by the security forces because of the hostage situation.
Earlier in the day, officials said some of the militants wearing vests loaded with explosives had formed groups of women and children and forced them to sit near them. Due to the presence of women and children with the suicide bombers, the operation was being conducted with utmost caution, they added.
A security source said that 30 militants had been killed so far in the clean-up and rescue operation, while 190 passengers had been rescued. Around 30 people who sustained injuries had been sent to hospitals.
He said two drivers in the main engine and eight security personnel were killed during the operation.
There was a huge explosion and firing, a scene that can never be forgotten, said Mushtaq Muhammad as he recounted the moment when militants attacked the train. Mushtaq was among the passengers rescued from the train, according to BBC Urdu service.
This is the first time the BLA or any insurgent group in the Balochistan province have resorted to hijacking a passenger train, although in the last year, they have stepped up their attacks on security forces, installations and foreigners in different parts of the province.
The security source said some of them were using satellite phones to remain in touch with their handlers.
The Pakistan Railways have set up an emergency desk at the Peshawar and Quetta railway stations as frantic relatives and friends try to get some information about their loved ones on the train.
Pakistan Railways had resumed train services to Peshawar from Quetta after a suspension of more than a month and a half.
The Pakistan media earlier reported intense firing and explosion near the tunnel, where the militants hijacked the train.
The insurgents claimed that they freed women and children. However, their claim was contested by officials, with Minister of State for Interior Talal Chaudhry saying the hostages were rescued by the security forces.
Rana Muhammad Dilawar, a district police officer in the area where the train was stopped, said the security forces had surrounded the area, but there were reports that the militants had taken some women and children as hostages.
The US Embassy in Islamabad strongly condemned the attack on the train, and the hostage-taking of passengers.
“We extend our deepest sympathies and condolences to the victims, their families, and all those affected by this horrific act. The Pakistani people deserve to live free from violence and fear,” it said.
Balochistan has witnessed an uptick in terrorist attacks over the past year.
