The popular TV presenter was suspended pending an investigation, the broadcaster said, without providing details.
Clarkson, who has been in trouble before for behavior and remarks deemed offensive and provocative, was given a so-called final warning last year following a racism row.
At the time, Clarkson said he avoided using a racist word while reciting a well-known nursery rhyme while filming the car show, but begged forgiveness from audiences after admitting that "it sounds like I did."
The BBC said the program will not be broadcast on Sunday.
In October, Argentina's ambassador to Britain demanded an apology from the BBC after the "Top Gear" crew faced violent protests for allegedly referencing the country's 1982 war with Britain over the disputed Falkland Islands. The crew was forced to flee the country
In 2011, the BBC apologized to Mexico after Clarkson and his co-hosts characterized Mexicans as lazy and oafish.