The BBC confirmed Andy Wilman had left the long-running series, but would not say whether or not the decision was related to the outspoken presenter.
Clarkson was suspended by the BBC last month during an internal investigation after he attacked Top Gear producer Oisin Tymon, splitting his lip and verbally abusing him, at a Yorkshire hotel.
Clarkson’s contract was not renewed, with director-general Tony Hall saying “a line has been crossed” and “there cannot be one rule for one and one rule for another”.
But the broadcasting veteran received widespread public support, including from friend David Cameron.
Mr Wilman’s departure came after the agent of Clarkson’s former co-presenter James May said he was still in talks with the broadcaster despite earlier reports that he had ruled out a return to the show without Clarkson.
In a statement, Mr May’s agent said: “Conversations regarding the future of BBC’s Top Gear are ongoing, James continues to be involved in those conversations however no plans have been 100% confirmed.”
Earlier this week, BBC2 boss Kim Shillinglaw said Clarkson would return at some point.