The accident occurred in the Sikhio district of Nakhon Ratchasima province, 230km northeast of Bangkok, on a train from the capital bound for Ubon Ratchathani province.
Transport Minister Phiphat Ratchakitprakarn said in a statement there were 195 people aboard the train, adding that he had ordered a thorough investigation.
The crane was working on a high-speed rail project when it collapsed and hit the passing train, causing it to derail and briefly catch fire.
Prime Minister Anutin Charnvirakul told the State Railway of Thailand to provide good compensation for families of the dead, adding in comments to reporters after being briefed at the scene: "We need to investigate... and take legal action."
The Italian-Thai Development Public Company Limited, which was contracted to build the rail segment, expressed regret for the accident and said it would provide compensation and relief to families of the casualties.
In March last year, a 30-storey building under construction in Bangkok by a joint venture including ITD collapsed, killing 89 people, after an 8.8-magnitude earthquake struck neighbouring Myanmar.
ITD president Premchai Karnasuta was indicted in August along with 22 others on allegations of negligence and breaching construction regulations.
The executive and 14 others denied wrongdoing when they were first arrested in May.
Images shared by the ministry showed train carriages overturned next to shrubland and firefighters extinguishing a blaze as smoke billowed out.
Earlier footage of the crash site verified by Reuters showed rescue workers trying to extract casualties from one of the mangled carriages, with some badly injured passengers already being loaded into ambulances.
The elevated high-speed rail project, one of several under construction in Thailand, was being built above the existing rail line.
Part of the collapsed crane is still propped up by the concrete stanchions built to support the new rail link, with debris dangling over the tracks below.
The construction is part of the Bangkok-Nakhon Ratchasima segment of the high-speed rail project linking the Thai capital with the southwest Chinese city of Kunming.
Recovery operations at the accident scene continued into Wednesday evening with Anutin saying the track needed to be cleared by the end of the week.
He noted that this was a major rail route and delays would hurt the regional economy.
Chinese Foreign Ministry spokeswoman Mao Ning said the government attached great importance to the safety of projects and personnel in Thailand and was looking into the situation.
"At present, it seems that the relevant section was under construction by a Thai enterprise. The cause of the accident is still under investigation."
The cross-country high-speed rail project will connect to China through Laos.
The government said last year that more than a third of construction had been completed in the segment connecting Bangkok to Nakhon Ratchasima, with the whole line to Nong Khai at the border with Laos ready by 2030.
17°C