BSkyB executives are understood to be furious after Mr van Miert suggested the proposed deal raises problems.
"I feel there is a problem. I am receiving a lot of letters from Manchester United fans asking me to intervene," he said in an interview with Le Monde, the French newspaper.
He admitted the European Commission has no power to intervene in the bid, pointing out that it was a matter for British competition authorities.
However, his intervention comes at a sensitive time in the takeover timetable. Peter Mandelson, Secretary of State for Trade and Industry, is considering whether the bid should be referred to the Monopolies and Mergers Commission. He has until Monday to decide.
Tony Banks, the Sports minister, and Chris Smith, Secretary of State for Culture, Media and Sport, have expressed reservations about the deal, while a group of backbench MPs have called on Mr Mandelson to block the takeover.
"As Mr van Miert says, this is a matter for the British competition authorities and we are confident it does not raise competition issues under the British rules," a spokesman for BSkyB said.
The precedent for media groups owning football clubs is already well established on the Continent. Canal Plus, the French pay-TV group, owns Paris St Germain, while Silvio Berlusconi, the Italian media mogul, controls AC Milan.
However, Mr van Miert's comments will be seen as a warning against the increasing commercialisation of sport in Europe. In the same interview, he expressed doubts about plans by Media Partners to set up a European Super League. "In principle, we cannot act against [the Super League] in the name of free enterprise. On the other hand, their move must respect certain rules," he said.