The chatshow and radio host is said to have "jumped before he was pushed" after director general Mark Thompson chose not to renew his current contract, which ends in July.
It has been alleged that the development came following pressure from the BBC Trust and was influenced by the controversy surrounding Ross's prank calls to Fawlty Towers actor Andrew Sachs in 2008.
One BBC source told The Mirror: "48 hours ago we had a deal in place. We were happy, Jonathan's people were happy. Mark Thompson capsized the whole thing because he's running scared of the Trust. This is a purely political act to try to appease the BBC bashers."
Meanwhile, another insider told The Sun: "The Sachsgate thing just brought it all into focus and made Ross a stick to beat the BBC with. The feeling from the senior people at the BBC was that having Jonathan on board meant we were always going to get flak."
Ross announced yesterday that he was to leave the corporation after 13 years. He later admitted that he will be "sad" to depart.