The train services to key cities like Chiang Mai and Ubon Ratchathani are now suspended.
It is likely that the suspended services will continue for at least two days.
SRT employees have staged a strike apparently in retaliation against the government's plan to liberalise cargo-train services in the country.
SRT acting governor Bancha Kongnakorn Wednesday apologised to people for the inconvenience.
"We are urgently negotiating with the SRT labour union," he said.
According to Bancha, 110 train drivers and 104 technicians - or about 10 per cent of them - have joined the strike. Their move has affected many routes.
Deputy Transport Minister Sansern Wongchaum said the government's plan would not affect the welfare and rights of SRT employees, nor it was about the privatisation of the SRT.
The abrupt halting of the services; at least five in the north, two in the south and three in the northeastern regions, left hundreds of passengers stranded at the stations.
Sawit Kaewwan, vice president of the railway's labour union said that the protest will continue until Prime Minister Surayud Chulanont steps in to cancel the draft bill.
"We don't know when we will stop the protest. We will adopt a strategy that all of our train officials take sick leave. We will also suspend more the train services in many parts," he said.
In northern province of Phichit, at least two northern trains stopped their service.
In Nakhon Sawan, the Chiang Mai train halted its service at 5am and the Tapan Hin - Bangkok train would not leave the station as scheduled at 5.30am.
Many passengers and students were left stranded at Phichit station Wednesday morning.
Phichit station chief Wissanu Chankrachang later told the passengers to use other means of transportation as there would be no trains heading to Bangkok on Wednesday.
For southern train services, southern-bound services stopped at the provincial railway station in Nakhon Si Thammarat as SRT employees joined the protest.
The trains which have left Bangkok Tuesday evening for Malaysia, Sugnai Kolok, and Trang, stopped at Nakhon Si Thammarat station.
Passengers were transported on buses to their destinations from the station.
Nakhon Si Thammarat station chief Banchob Phetchuay said it was not clear whether two trains, which are scheduled to leave Nakhon Si Thammarat for Bangkok on Wednesday, would be in service or not.
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