The Speaker allowed Adityanath to raise the issue soon after the Lok Sabha assembled for the day.
He told the House that some plainclothesmen entered the coupe he was travelling in the Vaishali Express and pulled him out of the compartment "like a criminal".
He claimed that some men in uniform came a few minutes later and detained him at Ghaziabad Railway station for more than three hours.
"I was pulled out like a criminal. Even my identity card of Member of Parliament was snatched. Is this the way to treat an MP. I seek your protection," he said.
The Speaker asked the government to send a factual report on the incident.