Uefa has backed English referee Howard Webb's decision to award Austria an injury-time penalty in their 1-1 draw with Poland on Thursday at Euro 2008.
Webb penalised Mariusz Lewandowski for holding Sebastian Prodl and Austria scored from the spot.
But Uefa's William Gaillard said: "We don't think it is controversial that a player is pulled down by the shirt and a penalty is given."
Gaillard, who is director of communications at Uefa, added: "It (Webb's decision) was certainly within the laws of the game."
Beenhakker believes that Webb's late decision was incorrect - and has effectively knocked Poland out of Euro 2008 after a defeat against Germany and the draw in Vienna. "I've never had a problem in 43 years of being in football but this is something I cannot understand," he said.
Beenhakker also accused Webb of trying to prove he was a "big boy", although Austria also had reason to be unhappy with the English officials as Poland's goal appeared to be offside.
Uefa's disciplinary body may take action against Beenhakker for his comments, while the referees' committee will decide if Webb and assistants Darren Cann and Michael Mullarkey will take charge of another game at the tournament.
Given that England are not at Euro 2008, it was seen as an opportunity for Webb's team to stay at the tournament until the latter stages.
Gaillard added: "The referees' committee analyses all the games and makes the appointments according to its own analyses and we don't interfere with the way they are managing officials in this tournament.
"For sure there is a better chance to referee the final matches as his national team is not there but that is a statistical chance.
"I wouldn't speculate about the decisions of our referees' committee."