Steve Clarke was subjected to chants of “sad fenian b*****d” from Rangers fans during Killie’s 5-0 defeat in the Scottish Cup fifth-round replay.
The ex-West Brom boss did not hold back after the game saying that people were still “living in the dark ages”.
He said: “I wake up every morning and I thank Chelsea for taking me away from the west. My children have nothing to do this with this, thankfully. My children and grandchildren. It’s fantastic to be back in Scotland.”
Kilmarnock have backed their manager’s comments.
“The board’s position is that they and everyone at the club is fully behind Steve in condemning sectarianism in all its forms,” a spokesman for the club said.
“There is no place for sectarianism in football or society.”
Rangers boss Steven Gerrard said his fans behaviour was “unacceptable”.
The Scottish FA issued a statement on the latest incident of “unacceptable conduct”.
On Sunday Killie striker Kris Boyd was subjected to sectarian chants from the Celtic support, while he was also struck with a coin.
Ian Maxwell, Chief Executive at the Scottish FA: “The Scottish FA condemns in the strongest possible terms the spate of incidents this season involving unacceptable conduct in Scottish football. This season we have witnessed match officials and players hit by coins, sectarian singing at matches and abusive and threatening behaviour towards match officials, players, managers and coaching staff. This behaviour is completely unacceptable and simply has no place in football, or indeed Scottish society.
“Football has a responsibility to take action. We must do all that we can under our current rules and engage with clubs to seek to eradicate such behaviour.
“This issue, however, is not one that football can solve on its own. To that end, SPFL Chief Executive Neil Doncaster and I recently met with Cabinet Secretary for Justice Humza Yousaf, Minister for Public Health, Sport and Wellbeing Joe Fitzpatrick and Police Scotland Assistant Chief Constable Bernie Higgins to discuss unacceptable conduct in football and how we can work together to address this.
“We will seek further discussions in light of the most recent events to maintain the momentum for change.”