According to a report in the Guardian, the email sent by Hartnett before the process began said the review would find "nothing of substance".
The email, which was marked "private and confidential – please do not pass on to anyone without coming back to me", was sent by Hartnett on 15 December 2011 to 10 senior HMRC officials.
The contents of the email also suggests Hartnett told his staff that the review by Sir Andrew Park would conclude no evidence of serious wrongdoing.
The inquiry into five major tax settlements by HMRC, including controversial deals with Goldman Sachs and Vodafone, concluded the final payments were “reasonable and the overall outcome for the exchequer was good”.
However, it criticised HMRC for governance failures, which the public spending watchdog said “confirmed our concerns over the processes by which the settlements were reached”.
Hartnett, who has since stepped down from the job, wrote that he had held a meeting with Morse, which was "useful and interesting".
"Amyas has been insistent that Andrew Park tackles the cases one at a time. He [Morse] has told me that he has made clear to the NAO that his expectation is that nothing of substance will be found in the review."
Despite Hartnett being somewhat vindicated by the review, the deals caused public consternation. HMRC senior representatives were hauled before the Public Accounts Committee and openly criticised to much media fanfare.
According to the email, Morse apologised for the way that HMRC officials had been questioned the MPs.
"He [Morse] did not envisage things playing out the way that they have and was sorry for the individuals in HMRC who had been bruised by the actions of the PAC and for the difficulties the department had experienced," Hartnett wrote.