Another 64 people were injured and rescuers on Wednesday were still searching the wreckage and giving first aid.
The derailment occurred on part of an ambitious planned high-speed rail project that will eventually connect China with much of Southeast Asia.
The crane, which was being used to build an elevated part of the railway, fell as the train was travelling from Bangkok to Ubon Ratchathani province, according to the public relations office for Nakhon Ratchasima province, where the accident took place.
Photos published in Thai media showed plumes of white then dark smoke above the scene, and construction equipment hanging down from between two concrete support pillars.
Rescue workers stood on top of overturned railways carriages, some of them with gaping holes torn on their sides, video from public broadcaster ThaiPBS showed.
What appeared to be sections of the crane were scattered along the track.
Meanwhile, paramedics gave first aid to injured passengers.
Thai media reported the train had three carriages, the last two being the most damaged.
Transport Minister Piphat Ratchakitprakan said 195 people were on board the train.
He said he had ordered an investigation.
The elevated segment that collapsed is a part of a Thai-Chinese high-speed railway project linking the national capital Bangkok to the northeastern province of Nong Khai, bordering Laos.
The two-stage rail project has a total investment cost of more than 520 billion baht ($A29 billion) and is associated with an ambitious plan to connect China with Southeast Asia under Beijing's Belt and Road Initiative.
In August 2024, a railway tunnel on the planned route, also in Nakhon Ratchasima, collapsed, killing three workers.
Days of heavy rain were believed to have been a factor in the collapse.
19°C