The Deputy First Minister denied the move by Leslie Evans had raised issues over accountability.
Ms Evans, the former permanent secretary, was in charge during the Government’s botched handling of harassment complaints against former first minister Alex Salmond.
She was invited to give evidence about her time in the role to the Scottish Parliament’s finance committee.
However, she rejected the invitation, leaving MSPs furious and "extremely disappointed”.
After a period of paid leave, Ms Evans retired from the civil service on March 31 and has been replaced by John-Paul Marks.
During a meeting of the finance committee on Tuesday, Tory MSP Liz Smith said the refusal raised two issues.
She said: "Firstly, that as yet this Parliament hasn't been able to scrutinise the previous permanent secretary about some of the issues that she felt had caused some difficulties within the administration process.
"But secondly, it has raised a concern about the accountability of the permanent secretary, whoever he or she may be, to the Scottish Government, but also to Parliament."
Mr Swinney argued the permanent secretary “isn't an individual, they are an office holder”.
He said: "So any of the questions that Liz Smith or the committee is interested in, can be put to the [current] permanent secretary, and I understand the permanent secretary is coming to the committee very shortly."
He said civil servants did not act in an individual capacity, but on behalf of ministers.
Mr Swinney said issues around the old complaints procedure had been "really openly scrutinised", including by a Holyrood committee last year.
Ms Smith said: "Do you accept that our work has been slightly compromised by the fact that, in a public session of committee, it's been difficult for us to know exactly what went on in terms of the processes and how that could have been better?"
Mr Swinney responded: "I don't share that view because of the fact that there was extensive scrutiny of that process undertaken by a specific parliamentary committee prior to the 2021 election, at which the former permanent secretary made, if my memory serves me right, more than one appearance."