The international development minister was stopped and searched at Washington DC's Dulles airport after a series of meetings on tackling terrorism.
Mr Malik, MP for Dewsbury, West Yorks, had his hand luggage checked for explosives when returning to Heathrow.
He said the same thing happened to him at JFK airport in New York last year.
On that occasion he had been a keynote speaker at an event organised by the Department of Homeland Security (DHS), alongside the FBI and Muslim organisations, to talk about tackling extremism and defeating terrorism.
Mr Malik said he had received numerous apologies and assurances from the US authorities after that incident.
But he was again searched and detained by DHS officials on Sunday.
Mr Malik said two other Muslims were also detained.
"I am deeply disappointed," he said.
"The abusive attitude I endured last November I forgot about and I forgave, but I really do believe that British ministers and parliamentarians should be afforded the same respect and dignity at USA airports that we would bestow upon our colleagues in the Senate and Congress.
"Obviously, there was no malice involved but it has to be said that the USA system does not inspire confidence."