The claim came after the Scottish Gamekeepers Association (SGA) questioned whether the charity should have published information about a police investigation into the death of a golden eagle in Deeside.
The RSPB, which was called in to help the original police inquiry, claimed the bird had apparently been caught in an illegal trap before being moved 10 miles while still alive.
But the SGA said its own investigation found no evidence to support the RSPB's theory, with a vet's report suggesting the injuries were only consistent with those which might have been caused by a trap.
The SGA, which sits with the RSPB on the Partnership for Action Against Wildlife Crime Scotland (PAWS), has called into question the RSPB's objectivity to act as an expert witness.
Duncan Orr-Ewing, head of species and land management at RSPB Scotland said he "rejected absolutely these unprofessional assertions of the SGA".
He added: "Our statement followed proper discussion and approval from the police and was in full accordance with our joint working protocol."
He claimed the official post-mortem report concluded the bird had suffered two broken legs due to trauma "that could be consistent with an injury caused by a spring-type trap" and that the severity of these injuries "would prevent the bird from being able to take off."
"This is a rather desperate statement from the SGA, which seemingly does more to reveal its true nature as an apologist for the worst types of wildlife crime, as it tries to defend the indefensible. Indeed, it calls into question its commitment to the aims and objectives of PAWS."
The golden eagle was found dead in May last year near Aboyne, Aberdeenshire. The RSPB put up a reward of £1000 for information leading to the arrest of those responsible.
The charity said the bird, which had been fitted with a satellite transmitter, had been apparently caught in an illegal trap in the Glen Esk area after arriving from Glenshee. It was moved nearly 10 miles while still alive to a country road, where it was found dead.
The SGA took the unprecedented step of conducting its own inquiry into the bird's death after voicing concerns over "irregularities in the interpretation promoted through the national media by the RSPB".
The SGA said detailed knowledge from those familiar with the operation and strength of traps suggested the theory put forward by the RSPB was highly improbable. It added there was a lack of substantive evidence to back claims the bird had been moved and left to die.
Nobody has been charged with the alleged crime.
The SGAhas presented its report to Paul Wheelhouse, Minister for Environment and Climate Change,.
A spokesman said the SGA had worked hard as an active partner in PAWS and was proud of the dramatic fall in the number of bird of prey abuse cases in Scotland but added: "The SGA feels it is important to call into question whether it is appropriate any singular organisation, with a clear political agenda, should be privy to such sensitive evidence under the guise of expert witnesses in crime cases.
"To be able to use privileged information, to which all other partners in PAWS are denied access, in order to make damaging media statements against a profession raises serious questions about fairness of process, particularly when police have found no clear evidence of criminality."