Cowan was due to appear on yesterday's Off The Ball radio programme but was replaced shortly before it went on air.
And the 44-year-old's position remains under review, as the Sunday Herald understands the BBC has yet to make a decision on when or if he can return to the airwaves.
A spokesperson from the BBC said: "Given the comments in his column, it would have been inappropriate for Mr Cowan to appear on the show."
Cowan's take on women's football came as the Scottish international team defeated their Bosnian counterparts 7-0 on Thursday night.
However, the pundit chose to slate the state of the women's game with a raft of insults and derogatory comments.
In yesterday's Daily Record column, headed And Now A Message From the Dark Ages, Cowan suggested that: "Fir Park should have been torched on Thursday in order to cleanse the stadium after it played host to women's football."
He then branded the women's game a "turgid spectacle" before describing two female players as "blokes".
He added: "Face it, folks, nobody cares about women's football. There was barely a thousand inside the ground, shocking for an international in ANY sport, and I guess putting the girlies head-to-head with Emmerdale and EastEnders was a bit daft."
Attached to the bottom of the column, an editor's note read: "Folks, we would like to point out Tam is a professional funnyman and what he has to say should be taken with a large pinch of salt.
"Also, his views are not necessarily those of the Daily Record as a whole."
Cowan's column provoked a heated response, especially from those involved in the development of women's football in Scotland.
Maureen McGonigle, executive administrator for Scottish Women's Football, branded Cowan's comments narrow-minded, claiming they had no place in the modern game.
She said: "I was very disappointed to read Mr Cowan's comments and I thought they showed extremely bad taste.
"It was a dreadful article and it was very narrow-minded. None of it was written from a place of fact and in no way was it funny.
"These girls sacrifice a lot to play for their national team, they need to take time off work and they certainly don't get the money the male footballers get.
"Yet they play for the sake of playing and so are ideal role models for young women to aspire to. That is something we should all be looking to support.
"And for someone to come along and mock the women's game in the manner in which he has is really disappointing. Furthermore, the justification from the newspaper - that they did not want to censor the man's opinions - is just a poor excuse."
The column also produced an immediate backlash on social-networking sites as many took to the web to share their dismay.
MSP Ruth Davidson, leader of the Scottish Conservatives, said: "Tam Cowan is going back to the 70s with his views on women's football."
Roseanna Cunningham, Minister for Community Safety, added: "All the great work going on to reduce abuse and violence is undermined in this article."
Meanwhile, Amy McDonald, head of youth development with Glasgow City FC, labelled the column "disgraceful".
"There are no words for the article," she said. "An opinion not rating women's football is fine but it's the content and sexism that is wrong.
"I am so disappointed. I would never disrespect the men's game like that.
"It was disgraceful, totally disrespectful and it speaks volumes about individuals and organisations such as the Daily Record."
Many in the entertainment industry also took the opportunity to refute Cowan's claims.
Comedian Jane Godley added: "I like Tam Cowan but am disappointed he turned into a 70s misogynist ranter and tried to pass it off as comedy Jim Davidson would be proud of.
"And if that is his opinion, then an editor shouldn't be apologising for it as a footnote."
Radio presenter Jim Gellatly said: "Tam Cowan's views on women's football. Surely he doesn't really believe this? Unbelievable."
Scottish political commentator Jeff Breslin added: "Big mistake from the Daily Record running that awful Tam Cowan piece. Get back to the dark ages with Andy Gray and leave the rest of us in peace."
Author and television produce Margot McCuaig said: "I am so annoyed that this has been allowed to go print. It's just a sexist opinion and shouldn't be in a national newspaper."