South Australian Hells' Angels' associate Reginald George Roberts will have to find $1.5 million in unpaid taxes and penalties plus hundreds of thousands of dollars in legal costs after the Federal Court dismissed his appeal against the ATO's pursuit of the missing millions.

But a criminal investigation into the alleged scam, believed by investigators to have tentacles across Australia and to have siphoned tens of millions of dollars of taxpayers' money into the pockets of motorcycle gang members, remains stalled.

The Commonwealth Director of Prosecutions has had a file on the case for two years but would not answer questions on Tuesday and the ATO said it could not discuss the case because of its privacy rules.

The Tax Office, which built its case over several years with the help of Federal Police, alleges Roberts got the ATO to pay out millions of dollars to trucking companies he ran either in his own name or through an alias between 2003 and 2006.

Trucking outfits nominally controlled by the convicted drug-runner claimed rebates on about $28 million worth of diesel between 2003 and 2006 and the Tax Office alleges that very little of the road haulage activity claimed by Roberts' companies actually took place.

But ATO insiders believe the Adelaide connection is just one link in a national network, cashing in on federal government subsidies to the trucking industry.

After authorities hit Roberts with tax bills and penalties of more $3 million, he launched legal action, first using the ATO's internal appeals process to have the bill reduced by about half.

He then continued his battle in the Federal Court, unsuccessfully arguing that he was innocent of any wrongdoing and saying the Tax Office has accused him of fraud without evidence and was guilty of "conscious maladministration".

But the Federal Court in Adelaide has thrown out Roberts' latest bid to appeal the Tax Office's decision and awarded costs against the truckie, leaving him with a potential legal bill running into hundreds of thousands of dollars.

But Tax Office sources say there is still frustration that federal law enforcement agencies have failed to act on evidence of larger a fraud network with national reach that has used dozens of haulage firms to operate an identical fraud as the one alleged against Roberts.

After nearly a decade gathering evidence of a scheme allegedly run by Hells Angels bikie gangs and extending to at least three states, investigators are frustrated that nobody had been arrested or charged.

They believe a larger organised crime operation went unchecked for years while it systematically defrauded fuel subsidies.

The nerve centre of the scheme is alleged to be an accounting firm in regional Victoria, owned for several years by Melbourne Hells Angels strongman Peter John "Skitzo" Hewat.

False claims provided to the Tax Office by bikies, sometimes using fake identities, claim generous Commonwealth rebates for diesel to run fictitious trucks owned by companies that exist only on paper.

The Tax Office has linked Roberts to Mr Hewat and the Victorian Hells Angels through the Victorian accountants, which he once owned and whose premises were used as a mailing address for a company alleged to have been controlled by Roberts through an alias.

The accountancy firm, which was raided by federal police as part of the investigation into Roberts, is linked to at least 50 other trucking companies around the country suspected of rorts against the rebate scheme.