No passenger injured in the mishap but there were mild injuries to the driver, police said.
All passengers were evacuated at Kasu Begu railway station, they said.
Heavy rains in Rajasthan lead to flooding, resulting in casualties and widespread disruption. Rescue operations are underway, and schools are closed in several districts.
The Railways cancelled 234 trains while 340 trains have been affected so far due to protests against the Agnipath scheme for recruitment in the defence services, the Railways said on Friday.
The Thar Express has been running between Jodhpur and Karachi since services resumed on February 18, 2006 after a 41-year suspension.
The bus service was first started in February 1999 but suspended after the 2001 Parliament attack. It was restarted in July 2003.
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