The 59-year-old's departure comes at the end of a traumatic few days at Rugby Park, which saw Johnston forced to deny allegations he had sought to discuss Jefferies' tactics with club captain Kevin Kyle.

The controversy proved to be the final straw for Jefferies and long-time assistant Billy Brown.

Killie said in a statement: "An agreement has been reached among Kilmarnock Football Club, team manager Jim Jefferies and assistant team manager Billy Brown, which will allow Messrs Jefferies and Brown to leave the employment of the club with immediate effect. The agreement was reached by mutual consent.

"Everyone at Kilmarnock Football Club wishes to thank Jim and Billy for their eight years of service to the club, a period which witnessed several top-six SPL finishes and the League Cup final in 2007.

"The club will now seek a new manager with a view to restoring its position in the top six of the SPL and challenging for this year's Scottish Cup."

Scotland striker Kyle last week alleged Johnston had "discreetly" asked him to discuss Jefferies' tactics, with the 28-year-old saying to have done so would have been going behind his manager's back.

Saturday saw Johnston deny instigating a conversation on the subject with Kyle, who also recently went public with his concerns about Killie's lack of a club doctor.

Johnston told BBC Radio Scotland: "If I wanted to talk tactics, I'd discuss it with the manager.

"It was a subject raised by Kevin."

Johnston said he would establish whether Kyle had been misquoted before deciding whether to take disciplinary action against the player.

Jefferies refused to comment on the controversy when contacted by Press Association Sport on Friday but was reported to be furious with his chairman, with rumours he was even contemplating legal action.

Johnston insisted his manager's anger was actually directed at Kyle, but Jefferies' departure suggests an irrevocable breakdown in his relationship with his chairman.

Killie, who are £9million in debt, have slipped to second bottom of the SPL after winning just one of their last nine games in what was becoming Jefferies' most difficult season in charge.

He saw his bid to add former player Gary Locke to his coaching team snubbed by Johnston in the summer.

That did not go down well with the players, who were also far from happy after Johnston imposed a new system of fines for yellow and red cards.

Today's news must also cast doubt on the future of Kyle, who is out of contract in May.

Johnston had planned to offer the striker an extension prior to last week's allegations.

Former Falkirk, Hearts and Bradford boss Jefferies was the SPL's longest-serving manager having taken charge at Killie in February 2002.

He led them to fourth place in his first full season at the helm, two more top-six finishes and a League Cup final in 2007.

A lack of resources at Rugby Park then began to tell, with the club ending 2007-08 second bottom of the table.

They finished eighth last term after Jefferies pulled off what many considered to be the signing of the season in Kyle.

Jefferies leaves Rugby Park with the club just two points behind rock-bottom Falkirk, ahead of Saturday's game with Motherwell who - along with Dundee United - are now one of three managerless SPL sides.

Jefferies had already been linked with the vacancy at Tannadice prior to leaving Kilmarnock and he is now likely to become the hot favourite to succeed Craig Levein.