Weekend newspaper reports in the Republic compared the recent bust-up between Indian coach Greg Chappell and national captain Sourav Ganguly to allegations of a poor relationship between Woolmer and Cronje.
But Woolmer denied this to Business Day, saying that he remained friends with the disgraced Cronje right up until his death in an aircraft accident.
"We had a problem with a practice he was unhappy about. Graeme Ford was my assistant at the time and we were at a net where Hansie was upset because he was not getting the attention he felt he needed with his batting," Woolmer told the newspaper.
"I had to intervene when he had a go at Graeme, but we never had an irretrievable break-up. I just don't know where that came from," said Woolmer, who is now the national cricket coach in Pakistan.
"I was still talking to Hansie, and had dinner with him shortly before he died. We had remained good friends. My problems at that time were more with the United Cricket Board than him," Woolmer said.
Woolmer is in South Africa on a break and had his own thoughts on the Chappell issue, having coached Pakistan for a little over a year now.
"There is a great deal of sensitivity among the people here, and it takes time to get to know them and understand their culture," said Woolmer, who has been with the Pakistan team for just over a year.
"My main thought on the Chappell issue - which does not really concern me - is that Greg perhaps went in too hard, too soon. "It is hardly my place to judge, but I think I would have waited, got to know the personalities involved, and developed an understanding of the way they worked, before pushing too hard."
"My main problem comes from sections of the media who are completely obsessive about cricket," said Woolmer.