The Top Gear presenter said that if immigration officials were allowed to "use their discretion" in order to wave certain passengers through, queues would move a lot faster.
As reported by The Daily Telegraph, Clarkson said: "Nobody is waved through any more. Immigration officials are not allowed to use their discretion.
"Common sense has been erased from the system, and the result is plain for all to see. There's a two-hour wait. The only possible solution is to introduce a bit of racism."
He went on to suggest that a "nice family of four coming back from their holiday in Sardinia" should be regarded with less suspicion than other passengers, and claimed that "bleeding-heart liberals" prevented officials from targeting only high-risk passengers.
"You can't get that sort of thing past the bleeding-heart liberals. They believe that... a hook-handed imam with fire in his heart and hatred in his eyes is just as likely to whip up anti-western sentiment as Joanna Lumley."
'Nobody likes a racist," he stated. "Nobody likes prejudice. It has no place at work, at play or on the terraces of a football stadium. It has no place at school, or in government.
'But at Heathrow Airport? Hmmm."
A spokesman for the Public and Commercial Services Union, which represents immigration officers, said: "Clarkson is an idiot."
Clarkson sparked controversy last year after he suggested that public sector strikers should be shot in front of their families.