The accident happened in Sikhio district, in Nakhon Ratchasima province, as the train was travelling from Bangkok to Ubon Ratchathani with nearly 200 people on board.
The crane, used to build an elevated section of a high speed rail line, fell onto the track, derailing the train and crushing several carriages.
At least 30 people were killed and dozens more injured. Emergency crews worked through the wreckage, dealing with fires and searching for victims.
The government has ordered an investigation into safety standards on the project, which is part of a wider rail link planned to connect Thailand with the region.
