The police watchdog looked into Dr Steven Peers's arrest by Insp David Kehoe in Salford in 2014, but cleared him of gross misconduct.
Greater Manchester Police (GMP) had disagreed he had a case to answer.
Greater Manchester Police Federation said the IPCC inquiry was "flawed".
Dr Peers was detained for failing to provide a breath specimen but the case against him later collapsed.
He was filming the arrest of a anti-fracking protester at Barton Moss in his role as a lawful observer when he was accused by Insp Kehoe of drink-driving.
He denied the charge and claimed video evidence showed he was wrongly arrested.
Footage of his arrest published on social media prompted GMP to refer the incident to the IPCC.
A GMP internal investigation found Insp Kehoe had no case to answer, but the IPCC deputy chair Rachel Cerfontyne directed that a gross misconduct hearing should take place.
The IPCC also found the officer had no case to answer in October 2016.
GMP Federation chairman Ian Hanson said his organisation commissioned an independent barrister to review the IPCC's inquiry.
He said the evidence in the report, which was sent to the police watchdog, suggests the investigation was "flawed from the outset" and there was either "gross incompetence or criminality".
Mr Hanson said he want to see an "independent, thorough investigation".
An IPCC spokesperson said the watchdog received a complaint, which has been "dealt with through our normal internal complaints process".
Anti-fracking protests began at Barton Moss in November 2014 when energy company IGas started test-drilling for shale gas.
The Independent Police Complaints Commission's (IPCC) inquiry into the conduct of an officer during a fracking protest was "potentially criminal", a police federation has claimed.