OTTAWA - The federal government is appealing a court ruling that overturned Justice John Gomery's findings against Jean Chretien and cleared the former Liberal prime minister of blame in the sponsorship scandal.

In papers filed Friday -- signed by deputy minister John Sims, the top-ranking bureaucrat in the Justice Department -- government lawyers argue that the Federal Court trial division was wrong to conclude in June that Gomery was biased against Chretien and his former chief of staff Jean Pelletier.

"We are extremely disappointed," said Peter Doody, one of Chretien's lawyers.

"We thought the (original) decision was not only correct in law but made good common sense . . . I would have thought they'd want to put this behind them, but clearly they don't."

The appeal notices in both the Chretien and Pelletier cases were filed late Friday at court offices in Montreal, about 90 minutes before the legal deadline for action was to expire.

The Justice Department referred queries to the Privy Council Office, where spokeswoman Myriam Massabki was unable to say why the government waited so long to appeal a verdict handed down three months ago.

The delay meant the appeals were filed in the midst of the federal election campaign, but it will likely be months before the case can be heard by the Federal Court of Appeal.

Gomery concluded, in the final report of his public inquiry more than two years ago, that there was no evidence Chretien or Pelletier did anything personally and overtly wrong.

But he said they were guilty of "omissions" in their oversight of the sponsorship program, in effect holding them politically responsible for the program that saw millions of taxpayers' dollars flow to Liberal-friendly advertising and public relations firms.

Gomery's findings were set aside by Justice Max Teitelbaum, who concluded in June that Gomery had demonstrated a "reasonable apprehension of bias" and prejudged the case in comments made to the media during and after the hearings at his inquiry.

The normally loquacious Gomery said Friday he was pleased with the federal decision to appeal the Teitelbaum ruling but otherwise curbed his tongue.

"I think the case deserved a second look and I think I'll limit myself to that," he said. "Anything else and I might get into dangerous territory."

The Gomery inquiry, which uncovered evidence of fraud and kickbacks in the sponsorship program, was widely credited with helping pave the way to power for Prime Minister Stephen Harper's Conservatives in the 2006 election.

Since then, however, relations between the Harper government and Gomery have been strained. The now-retired judge has publicly slammed Harper for failing to institute all the reforms he recommended to curb the power of the Prime Minister's Office in an effort to avoid future abuses.

Gomery was also harshly critical of Harper for delaying an inquiry into the business dealings of formed Tory prime minister Brian Mulroney and German-Canadian arms dealer Karlheinz Schreiber. That inquiry is not expected to begin hearing testimony until early next year.

Teitelbaum, in his ruling in June, said Gomery's zeal to remain in the media spotlight at the sponsorship inquiry trivialized the proceedings and undermined his findings against Chretien and Pelletier.

"This preoccupation with the media outside the hearing room had a detrimental impact on the fairness of the proceedings," wrote Teitelbaum.

His scathing conclusion was that, given Gomery's media comments, "no reasonable person, looking realistically and practically at the issue and thinking the matter through, could possibly conclude that the commissioner would decide the issues fairly."

The Conservative government downplayed the ruling at the time as a narrowly procedural one and claimed it did nothing to relieve Chretien of political responsibility for the sponsorship affair.