Blues were denied a penalty when Clayton Donaldson appeared to be fouled by Ben Marshall just before Danny Graham doubled Blackburn's lead.
"You look back to the biggest moment in the game, that would have turned it on its head and the officials didn't do their jobs properly," he told BBC WM.
"The referee said [Donaldson] went down easily then said there was no contact."
Rowett continued: "There was another big decision when Jordi Gomez went right over top of the ball against Stephen Gleeson, which was a disgusting challenge.
"There's a massive gash down Gleeson's leg. The referee is 10 yards away, he decides to have a lovely little chat with Gomez about it but doesn't book him. I have to say I think it's the most inept officiating I think I have seen this season.
"I'll see the referee and ask his opinion [about the incidents]. He'll do what they usually do and say 'sorry if I've made a mistake, I apologise'. But it doesn't make any difference, it's not going to get us the points back."
Rowett was also critical of his team and was particularly unhappy with their defensive shape, having seen them concede their fourth goal in two games on the road.
"There's no excuse, it's very poor defending." he said. "The first goal [comes from] a ball that bounces in between two of our defenders in the box and we don't deal with it."
Manager Gary Rowett says Birmingham were the victims of "inept officiating" in Tuesday's 2-0 defeat at Blackburn.