The Secretary of State for the Environment insisted the Government would not be able to implement such a policy even if it wanted to.
The controversy started in December when the Government capped 2005/6 recycling targets at 30% and cut the fine for non-compliance with the Landfill Allowance Trading Scheme (LATS) to £150 per tonne.
Doughty said the law changes were calculated to "give preferential help to Labour-run councils" but Beckett has dismissed the claim.
Beckett told MRW: "It is a very strange idea. All the work on deciding what the level of fines should be is carried out by impartial civil servants.
"There is no policy direction that this should be done to benefit anyone, nor could there be and nor would civil servants adhere to it if there was."
More than 100 councils saw their recycling targets reduced by the 30% cap, and many authorities are concerned they will not be able to comply with LATS.