A story in The Mirror today claims that the duo were annoyed when Cowell turned up two hours late at BGT auditions and that the rift has festered because the reality TV mogul has failed to apologise.
When Ant & Dec discovered Cowell was late over an extended bath session, they were apparently "unimpressed with his rudeness".
"They know he goes in for power games and posturing, and they hate it. Ant and Dec feel they are on a different level and should not be treated in that way," said a source.
The paper claims that the two parties have reached a truce after finally reaching an agreement on a second series of Cowell's gameshow Red or Black?, but there are allegedly still tensions between the trio.
However, spokespeople for Ant & Dec, Cowell and Got Talent have rubbished the accusation, insisting that Cowell's well-known bad habit for arriving late for events and filming was taken in good humour.
"Ant and Dec know Simon starts filming late and have joked about it. No-one has fallen out," said a rep for the ITV1 talent show.
Ant & Dec's statement reads: "All three are good friends and have a fantastic working relationship."
Britain's Got Talent launches on Saturday, March 24 at 8pm on ITV1.
> 'Red or Black?' second series confirmed: Potential £3.5 million winner
> Simon Cowell promises 'cooler' 'Britain's Got Talent'