The chief constable of West Yorkshire police will be investigated by the police watchdog following disclosures about the conduct of officers, it emerged on Saturday.

The independent panel report into the Hillsborough tragedy suggested Sir Norman Bettison may have been part of a "black propaganda" operation to smear football fans to cover up for failings of South Yorkshire police where he was an inspector in 1989.

A meeting of West Yorkshire Police Authority's special committee on Saturday agreed to record a complaint against the chief constable and immediately referred it to the Independent Police Complaints Commission (IPCC) for investigation.

Special committee chairman Richard Baldwin said: "A number of factors led to the committee taking the decision to refer the complaint to the IPCC, including the gravity of the subject matter, the wholly exceptional circumstances, and a pressing need to maintain public confidence in both policing governance and the police complaints system. It is important that the facts are fully established and evidence considered from other sources before any further decisions are taken.

"The IPCC, as an independent body with a statutory duty to uphold the police complaints system, is best placed to conduct such investigations."

On Friday, Sir Norman issued his second statement in 48 hours on the affair after again criticising Liverpool football fans. The deputy prime minister, Nick Clegg, said his words flew in the face of the damning conclusions of the Hillsborough independent panel.

Within hours of the Liberal Democrat leader's intervention, Bettison issued a statement apologising if the families of the 96 who died had been upset by his remark that "fans' behaviour … made the job of the police in the crush outside Leppings Lane turnstiles harder than it needed to be".

The words were included in a statement – issued after the report was published this week – in which he made clear he was staying in his post despite the independent report revealing further details about his key role in a South Yorkshire police internal review team condemned as a "black propaganda" unit.

The storm grew as his employers, the West Yorkshire police authority, began an investigation into matters that the report raised about his role. Asked about Bettison's position, Clegg said: "His words were ill-judged. That is obvious. After a report like that, to suggest the fans were an impediment to the police operation when the report revealed the truth that the burden of responsibility lay with the police and other emergency agencies was insensitive and ill-judged.

"He will need to react pretty clearly to clarify what he meant. It flies in the face of the basic thrust of the report."

Within hours, Bettison apologised. "Let me speak very clearly," he said. "The fans of Liverpool football club were in no way to blame for the disaster.

"I formed this clear view on hearing all the evidence that was presented at the Taylor inquiry.

"The evidence was overwhelming. The police failed to control the situation, which ultimately led to the tragic deaths of 96 entirely innocent people. I can be no plainer than that and I am sorry if my earlier statement, intended to convey the same message, has caused any further upset.

"My role was never to besmirch the fans. I did not do that. I am deeply sorry that impression and slight has lingered for 23 years."

The Hillsborough independent panel, which had unprecedented access to 450,000 documents, uncovered the true scale of the South Yorkshire police cover-up, which began in the hours after the fans were crushed to death at Hillsborough on 15 April 1989.

Fresh evidence in the panel report showed 164 police statements were doctored, victims were tested for blood alcohol levels and checks were carried out on the police national computer to access criminal records in order "to impugn the reputation of the deceased".

Criminal charges may now be laid against serving and former officers after South Yorkshire police set in motion a referral to the IPCC.