The massive crane's broken structure was left resting on giant concrete pillars, while smoke rose from the wreckage of the train below, footage from the scene verified by AFP showed.
Rescuers worked to extract passengers from the tilted carriages in Nakhon Ratchasima province, northeast of the capital Bangkok.
Mitr Intrpanya, who was at the scene, said he heard a loud noise "like something sliding down from above, followed by two explosions".
"When I went to see what had happened, I found the crane sitting on a passenger train with three carriages," the 54-year-old told AFP. "The metal from the crane appeared to strike the middle of the second carriage, slicing it in half."
The health ministry said in a statement that 28 were killed and 64 people were hospitalised, seven in serious condition.
The accident happened at a construction site that is part of a more than $5 billion project backed by Beijing to build a high-speed rail network in Thailand.
It aims to connect Bangkok to Kunming in China via Laos by 2028 as part of China's vast "Belt and Road" infrastructure initiative.
- 'Only company in charge' -
Engineering consultant Theerachote Rujiviphat, an adviser on the high-speed project, told AFP the Thai company contracted to build the section of the high-speed rail where the crane fell, Italian-Thai Development, was solely responsible for its collapse.
Theerachote, from the China Railway Design Corporation, said the launching crane that fell onto the existing rail tracks also belonged to Italian-Thai Development.
"It is the only company in charge. A similar accident also happened a few years ago under their responsibility," Theerachote added.
A representative for Italian-Thai Development, one of Thailand's biggest construction firms, said the company could not immediately answer questions from AFP.
Thai Prime Minister Anutin Charnvirakul said authorities must determine the cause of the crane collapse and hold those responsible to account.
"These kind of incidents happen very regularly," he told reporters in Bangkok.
"I have heard that it is the same company (involved in previous accidents). It is time to change the law to blacklist construction companies that are repeatedly responsible for accidents."
Italian-Thai Development and its director were among more than 20 people and firms indicted in August in a case linked to the collapse of a Bangkok high-rise in an earthquake. The collapse killed around 90 people, mostly construction workers.
China's foreign ministry said Beijing was looking into what happened on Wednesday, and "attaches great importance to the safety of this project and its personnel".
"Currently, it appears that the relevant section is being constructed by a Thai company," spokeswoman Mao Ning said at a regular press briefing.
Mao also extended China's "condolences for the casualties resulting from the accident".
- Deadly accidents -
The Nakhon Ratchasima provincial public relations department said the crane collapsed onto a train travelling from Bangkok to Ubon Ratchathani province, "causing it to derail and catch fire".
Thatchapon Chinnawong, the Sikhio district police chief, told AFP that authorities had resumed the rescue operations after briefly pausing due to "chemical leakage" at the scene.
Transport Minister Phiphat Ratchakitprakarn said 195 people were on board the train and authorities were rushing to identify the deceased.
Thailand has around 5,000 kilometres (3,107 miles) of railway but the run-down network has long driven people to favour travel by road.
Upon completion of the 600-kilometre high-speed railway, Chinese-made trains will run from Bangkok to Nong Khai, on the Mekong River border with Laos, at up to 250 kilometres per hour.
In 2020, then Thai prime minister Prayut Chan-o-Cha, who pushed closer ties with Beijing, signed a deal for Thailand to cover all expenditures for the project, while using China-advised technology.
Industrial and construction site accidents are common in Thailand, where lax enforcement of safety regulations has led to deadly incidents.
In 2023, a freight train killed eight people after it struck a pickup truck crossing railway tracks in eastern Thailand.
burs-tak-pk/sco/jm
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