The supporters' organisations feel the League should support them as they are helping its court case against the Office of Fair Trading over the television rights to the Premiership.
United's supporters' association may withdraw its support if the League does not reciprocate. The League is understood to be surprised by the timing of the objection and believes the two issues are separate.
A League spokesman, Mike Lee, said: "The issues at stake in our current court case remain the same. The supporters' organisations have recognised that the OFT pose a real threat to the fabric of the game. It would be wrong to trade support on other issues."
The League is understood to feel the BSkyB takeover raises serious concerns which are down to the competition authorities to deal with. This is not satisfactory for the fans' groups, and they want the League's co-operation.
The chairman of United's supporters association, Andy Walsh, said: "When the Premier League approached us to give evidence in the OFT case we saw it as the only way to retain some form of redistribution of wealth and parity within the Premier League. We're now reconsidering our position."