Days before voters head to the polls to narrow the field of mayoral candidates, incumbent Thomas Menino has been thrown into damage control mode as city officials attempt to get out from under the controversy over employees regularly deleting their e-mails, a potential violation of the state’s public records law.

Secretary of State William Galvin has ordered the city to find the e-mails of top Menino aide Michael Kineavy.

Menino’s rivals have pounced on the controversy, stirring up a firestorm that started with a Boston Globe report in which city officials said they could not provide Kineavy’s e-mails because of a “glitch” in the city’s computer system, which did not back up Kineavy’s e-mails after he deleted them both from his inbox and his deleted items folder. City officials say the flaw, which apparently existed for four to five years, has since been temporarily fixed and they’re working on a more permanent solution.

“This is a pure mistake, not intentional by anybody,” Menino told reporters, pledging to cooperate with Galvin and others.

But all three Menino opponents – City Councillors At-Large Michael Flaherty and Sam Yoon and South End contractor Kevin McCrea – have called for a criminal investigation, saying the episode has a whiff of corruption and purposeful wrongdoing, which city attorneys have denied. Yoon and Flaherty, who has led the charge for investigations, have asked Attorney General Martha Coakley and Suffolk County District Attorney Daniel Conley to also look into the matter.

“Common sense would say this is deliberate,” Yoon said at a Monday night forum. “There’s confusion about the basic technology of e-mail in our city.”

City Councillor At-Large Stephen Murphy, a Menino supporter, said he was skeptical of any charges of wrongdoing, pointing to the FBI hitting City Hall with questions last year over any involvement with the bribery charges leveled against former Sen. Dianne Wilkerson (D-Roxbury) and District 7 Councillor Chuck Turner. (Prosecutors have said the Menino administration is not a target in the case.)

“Everybody’s e-mails got subpoenaed,” Murphy said. “It seems to me the federal government would’ve uncovered something last year if there was a deliberate attempt to conceal something.”

Yoon and Flaherty, a former prosecutor, are both calling for a hearing into the matter, with Flaherty arguing that the deletion of e-mails puts the city at risk for lawsuits.

The issue will likely land in the City Council’s Government Operations Committee, which is chaired by District 3 Councillor Maureen Feeney. But if history is any indication, a hearing could be put off because the investigation into the e-mail deletions is ongoing.

The controversy has led to the three opponents teaming up over the issue of government transparency, though hours later McCrea quickly returned to form, criticizing the two councillors after a Monday press conference outside City Hall where the three decried the deletion.

“Now that they’re running for office, they say that they care about transparency,” McCrea said of Yoon and Flaherty at a Monday night mayoral forum co-sponsored by the Ward 4 and 5 Democratic Committees.

With Menino expected to easily top the ballot on Sept. 22, the fight for second place – and the chance to face the 16-year incumbent on Nov. 3 – appears to be between Flaherty and Yoon, who have largely maintained an informal truce and focused their attacks on the mayor.

“I haven’t seen them lay a finger on each other,” said District Councillor John Tobin of West Roxbury. “I’m surprised by the congeniality. It’s almost like they’re not running against each other.”

Political observers say the election will likely come down to turnout in neighborhoods of color, with Boston recently becoming a minority-majority city.

A diverse crowd of candidates running for City Council At-Large – made up of six blacks, two Latinos, and a Vietnamese-American – could significantly boost turnout in those communities, which would be a boon for Yoon.

“It’s all about the communities of color,” said one political operative working on one of the City Council campaigns. “That’s the only variable of this election.”