Boyle said the words in an episode of his Tramadol Nights series shown on Tuesday.
Broadcasting watchdog Ofcom is already investigating Boyle’s show after he made a controversial joke about Katie Price’s disabled son.
Tory MP John Whittingdale said the Scottish comedian should not be allowed to continue with his brand of humour.
“The words nigger and Paki are deeply offensive to a large number of people. I don’t think even in comedy it is justified,” he said.
“Frankie Boyle is becoming a serial offender. I really think Channel 4 will have to think whether it’s appropriate to screen programmes which are regularly causing offence to a lot of people.
“It might be a breach of the Broadcasting Code. Ofcom will have to determine that.”
But Channel 4 said the use of the words was “satirical”, not racist.
A spokesman said: “Channel 4 strongly refutes any suggestion we are endorsing or condoning racist language by our broadcast of Frankie Boyle’s Tramadol Nights.
“This cutting-edge comedy is clearly intended to ridicule and satirise the use of these words — Frankie Boyle was not endorsing them.
“Channel 4 would not have broadcast these words had they been used in a racist way. All the jokes highlight the unacceptable nature of this language.”
The spokesman added that strong warnings about the content were made ahead of the programme and Channel 4 received one complaint about racism following the broadcast.