The National Audit Office says it is carrying out fresh research that could contradict the Treasury's assessment of the £1.4m lifetime pension fund limit.
Chancellor Gordon Brown has said he might drop the entire pension simplification programme if the NAO finds against him.
Many industry figures had seen the referral to the NAO as a rubber-stamping exercise but the body – which functions independently of the Government and answers only to MPs – says it will not use the Treasury's figures as a starting point.
But critics of the Treasury's original figures say it has already given some ground by adopting a 20:1 approach on calculating the value of final-salary pensions and reducing the level of the penalty charge.
The NAO is checking whether 5,000 people would be hit by the cap at the introduction date of April 2005, with a further 1,000 who would not have been hit by the earnings' cap likely to be hit each year.
National Audit Office spokesman Barry Lester says: “We are gathering new data and embracing new material for this review, so yes there is a real chance of a different outcome to the results produced by the Treasury. We are entirely independent and can say whatever we wish.”
Scottish Life group head of communications Alasdair Buchanan says: “The way that the Treasury changed the assumptions before referring to the NAO has made it a lot easier for them to come up with the right answer.”