Flaherty acted after Ethics Commissioner Mary Dawson told him on Thursday that he had been wrong to send regulators a letter in his capacity as finance minister, and formally ordered him to refrain from writing similar letters without her approval.
Her order is an embarrassment for a Conservative government that came to power in early 2006 promising greater accountability in politics.
Flaherty urged the Canadian Radio-television and Telecommunications Commission last March to grant a radio license to a company based in his parliamentary constituency of Whitby-Oshawa, just east of Toronto. The rules allow regular legislators to lobby regulators, but ministers may not in their capacity as cabinet members.
"The letter ... was fully intended to be written and sent in my capacity as member of Parliament for Whitby-Oshawa," Flaherty said in statement emailed to Reuters. "However, due to an oversight my ministerial title was used in the signature block. This is regrettable and I can assure the ethics commissioner that this will not happen again."
Flaherty's constituent did not win the license to operate the radio station.
Dawson sent Flaherty a formal compliance order late on Thursday telling him that "it is improper for you as minister of finance" to have written to the regulators.
"I therefore order you to refrain from writing any similar letters in the future without seeking approval from my office," she said. Flaherty has been finance minister since the Conservatives took power.
Dawson's website shows she has issued only four such orders in the past three years, and Flaherty is the only cabinet member to have received one.
Thomas Mulcair, head of the main opposition New Democratic Party, said he has written to Prime Minister Stephen Harper to demand a probe into Flaherty's letter.
"The Conservative Party promised over six years ago that 'The time for accountability has arrived'," Mulcair said in a statement. "It's time to close the gap between promises and reality. It's time to take the first step by investigating the actions by Mr. Flaherty and start holding your ministers to account when they break the rules."
Last March, Dawson ruled that Industry Minister Christian Paradis had violated ethics rules by telling bureaucrats to set up a meeting with a former Conservative legislator who wanted to do business with Ottawa. She did not issue a compliance order against him.
(Editing by Vicki Allen, Janet Guttsman and Peter Galloway)