Ruth Parsons's tenure at the heritage agency included allegations from staff of bullying. Seven months after she left it was calculated she had accrued pension scheme benefits making her eligible for about £35,000 a year plus a £105,000 lump sum on retirement.
Ministers have now been urged to come clean over how approval was given for her severance package, which amounted to nearly three times her annual salary.
The 51-year-old was appointed to head the agency in 2009 but her time in charge was tainted by staff allegations of bullying. She had been a civil servant with the UK and Scottish governments for 30 years by the time she left.
Historic Scotland said no formal complaints were lodged, but a series of senior staff decided to leave the organisation after she took over the helm.
MSPs were shocked by the development and said the Scottish Government needed to be more transparent about the case.
Alex Johnstone, the Scottish Conservatives' spokesman on Infrastructure, Capital Investment, Housing and Transport, said ministers had to "come clean on who approved this and why".
He said: "Taxpayers will be rightly appalled by the excess of this golden goodbye payment.
"It's an insult to hard-working families everywhere for public money to be lavished on someone who, it appears, has chosen to leave of her own accord. How can the Scottish Government possibly justify giving someone a pay-off nearly three times her annual salary on top of a substantial pension package?"
Scottish Labour's Patricia Ferguson, the Shadow Cabinet Secretary for Culture, Sport and External Affairs, added: "The level of payout seems grossly excessive when considering the period of service at Historic Scotland and its dysfunctional nature during that period.
"This payment raises more questions about how Historic Scotland is managed. I have increasing concerns about how it is being run and given those concerns the decision of the SNP to give it even more responsibilities seems to go against best practice. Taxpayers will expect answers about how our money is being used."
Ms Parsons was appointed in 2009, and in October 2001 a staff survey revealed claims by staff that they faced harassment at work. The wellbeing study of Historic Scotland's 1100 staff at the time found 53 [5%] reported some form of bullying. Five said they were often victimised and two felt they were always bullied.
Ms Parsons, deputy director of the Strathclyde International Public Policy Institute at Strathclyde University, has always strongly denied allegations of discontent within the organisation, including "bullying" accusations levelled at her personally.
A Scottish Government spokesman said in a prepared statement: "Ministers do not approve individual severance packages. The approval is given to the Scottish Government to run a severance scheme to which people can apply. All applications are assessed against agreed criteria and Ms Parsons application for early exit was approved within the terms of this criteria."
Compensation is not normally payable "when someone resigns voluntarily outwith any existing (and approved) scheme" of compensation under government rules. Ministerial clearance must also be obtained.