Chief information officer Deepak Singh was paid £149,500 by HMRC to work three months beyond his leaving date.
Revenue & Customs paid senior official Singh the six figure sum for the period 19 June 2009 to 18 September 2009, accounts filed by the tax office show.
Singh had a three year contract at HMRC earning £160,000 per annum, ending in June last year.
However, for three months from 19 June to 18 September, HMRC paid Singh £149,500 through his company Orwell Consulting.
Listed under "Third party payments for services of a senior manager", HMRC's accounts show £149,500 was paid to Orwell Consulting Ltd "for the services of Deepak Singh (a director of that company) who held the position of Acting Chief Information Officer".
Singh said he informed the tax office of his daily rate and it was "willing" to pay it, according to reports.
HMRC's decision to allow Singh to be paid through his consultancy business would have substantially cut the former CIO's tax liabilities.
Singh is liable for corporation tax of up to 28%, significantly lower than the higher-rate of income tax of 40%.
HMRC is reported as saying it will ensure no tax is avoided as a result of the arrangement.
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