On Tuesday, federal prosecutors charged a D.C. tax office employee with stealing about $414,000 from the city coffers. Mary Ayers-Zander did it, charging papers state, by making fraudulent manual adjustments to legitimate taxpayers’ income tax withholding, resulting in payments to personal accounts she had set up.

In other words, Ayers-Zander found a weakness in the system and exploited it, finding a way to enrich herself because the internal controls within the Office of Tax and Revenue were not up to par, according to court records..

That modus operandi should sound familiar: It comes less than four years after the unveiling of the greatest fraud in District government history — the two-decade, $48 million scheme engineered by OTR middle-manager Harriette Walters that sent fraudulent property tax refund checks into the personal accounts of Walters and her co-conspirators.

Ayers-Zander’s alleged wrongdoing began in February 2007, about eight months before the Walters scam was uncovered. She had worked as a city employee since 2001, recently earning $52,590 as a “tax examining technician.” And despite the pledges after the Walters scam was uncovered — Chief Financial Officer Natwar M. Gandhi himself referred to it as a “major management failure” and pledged to remain as CFO in order to fix the mess — her alleged scheme is said to have continued nearly four more years unabated.

A spokesman for Gandhi noted that it was a tax office employee that uncovered the scheme earlier this year. That is well and good, but it proceeded during a time when independent auditors continually cited the tax office for its lax internal controls.

In 2008, reviewing the fiscal year in which the Walters fraud was uncovered, BDO Seidman auditors found a “material weakness” in the tax office’s financial controls, writing that the CFO’s office “may have elements of an anti-fraud program, but it does not seem to have as coordinated and comprehensive an anti-fraud program as it should given its size and complexity.”

Inspector General Charles Willoughby wrote city officials about the findings, telling them it was “imperative that management address the deficiencies in the report in order to maintain the financial integrity of the city.” Later that year, an investigation into the Walters fraud commissioned by the D.C. Council found a “culture of apathy and silence” inside the tax office and made a series of recommendations, which included “evaluat[ing] the use of manual processing functions ... that may exist in other parts of the organization.”

The next year, independent auditors downgraded the tax office issues a notch, deeming them a “significant deficiency” in need of attention. Still, in March 2009 congressional testimony, Willoughby renewed calls for “an intensified anti-fraud program.” And in 2010, auditors renewed their concerns. Their report, in fact, detailed how a mentally ill woman gained access to taxpayer accounts by filing change-of-ownership forms and submitting false tax returns. And in a finding that hinted at the sort of fraud allegedly perpetrated by Ayers-Zander, the auditors found that “adequate controls do not exist over the release and re-issuances”of certain tax refunds, noting that no fewer than 258 employees had the ability to issue refund checks without oversight.

This year, with KPMG replacing BDO Seidman as independent auditor, they again found a significant deficiency in the tax office — including “insufficient control procedures over the reconciliation of tax withholdings to taxpayer submitted data.”

In the wake of the new charges, and another large chunk of taxpayer money gone missing, it renews questions about management in the CFO’s office. It might be encouraging that an internal review led to these latest charges, but after four years of having another fraud go undetected amid the repeated warnings of auditors, taxpayers are justified in wondering what took so long.

Gandhi has undoubtedly made some moves to root out wrongdoing: He announced a package of reforms immediately after the Walters arrest and, a month later, a special audit committee to review internal controls. But his efforts to remake the tax office’s culture appear to have been incomplete.

David Umansky, Gandhi’s spokesman, said the arrest is proof that the post-Walters reforms are in place and working. The fraudulent actions that Ayers-Zander is accused of, he said, were infrequent and involved small amounts that were not subject to automatic reviews. A subsequent review of those refund transactions found a “pattern of suspicious adjustments.”

Suspicions were raised in January, Umansky said, and the case turned over to federal authorities. FBI investigators opted to watch Ayers-Zander to see if she had any accomplices in the office; when investigators were satisfied that she didn’t, he said, she was moved into a job where she had no control over funds and later fired.

Suggestions that the fraud should have been noticed sooner, Umansky said, are ill-founded. He noted that the tax office is installing a new computer system “that will eliminate whatever issues remain.”

”This one could never happen again,” he added.

Perhaps so, but the latest news comes with political ramifications. Gandhi, who has served as chief financial officer since 2000, enjoys good relations with Mayor Vincent C. Gray (D), most D.C. Council members and congressional overseers. But his current term will end next June, and he has not indicated whether or not he will be seeking another one, which would require a mayoral nomination and council approval.

Longtime reporter Jonetta Rose Barras wrote this in 2009, after covering another round of auditors’ warnings: “Residents forgave Gandhi when money walked out his shop the first time. He can bet if it happens again, even in a smaller amount, mercy and forgiveness will be on vacation.”