Sources said he was accused of hitting the producer in an incident last week, and the remaining three episodes of the current series might not be broadcast.
The BBC confirmed one episode – due for broadcast on Sunday – would not be shown, but gave few further details.
Clarkson, 54, has not commented, but has been joking on social media about films that could replace Sunday’s show.
He was given what he called his “final warning” last May after claims he used a racist word during filming.
At the time, he said the BBC had told him he would be sacked if he made “one more offensive remark, anywhere, at any time”.
In a statement earlier, the BBC said: “Following a fracas with a BBC producer, Jeremy Clarkson has been suspended pending an investigation.
“No-one else has been suspended.
“Top Gear will not be broadcast this Sunday.
“The BBC will be making no further comment at this time.”
BBC News special correspondent Lucy Manning said sources had confirmed reports Clarkson was suspended for “allegedly hitting a producer”.
“The incident is believed to have happened last week, but was reported to the BBC on Monday and dealt with on Tuesday,” she added.
“The next two episodes of Top Gear will not be broadcast and it’s understood that a third programme, the final of the series, is unlikely to be transmitted.”