Images of some of the Croatia squad bathing naked in their hotel pool, taken by photographers hiding in nearby bushes, were picked up by reporters and published online.
"I can't force them to be at your disposal after what you have done to them and their families," an angry Kovac told reporters at the team's training base.
"How would you feel if someone took naked pictures of you? They are adamant that they won't speak to you lot any more and I don't know whether the silence will end tomorrow or last until the end of our World Cup campaign.
"I respect my players' opinion and I also know that you have done a very professional job so far but you blew it with this one. The whole world has seen the photos."
Croatia lost their opening Group A game 3-1 to Brazil, and next face Cameroon on Wednesday.