The charges are being laid against a chartered accountant and two former employees at the federal agency's Montreal office.
The RCMP announced Thursday that the accused are suspected of participating in a scam where the functionaries pocketed hundreds of thousands in bribes, in exchange for helping to lighten people's tax loads.
The Mounties said the men also used the money to corrupt employees working under them. Thursday's arrests were tied to alleged crimes that, according to the police, defrauded the government of $4.5 million.
"Several components of the investigation are still ongoing and additional arrests and charges are expected," the RCMP said in a statement.
Francesco Fiorino is the accountant charged, and he faces 34 criminal counts in the case. Gennaro Di Marzio and Nicola Iammarrone, the federal employees, face 11 and 12 charges each.
A fourth suspect has been arrested for questioning. Charges could be laid against him.
The ongoing, years-long investigation has seen 11 arrests so far.
In a series of arrests last year, charges were laid against four people: a CRA auditor, an accountant, and two construction bosses including the scandal-tainted magnate Tony Accurso. Police pegged the size of the alleged fraud in that series of arrests at $3 million. Fiorino was also charged in last fall's roundup.