Rural Development Minister Ross Finnie has been quizzed by MSPs on a decision to relocate civil service jobs from Edinburgh to Inverness.
Great Glen House is the new base for SNH
The Scottish Parliament's audit committee called Mr Finnie to give evidence - the first time it has asked a minister to do so.
Labour MSP Susan Deacon and Lib Dem MSP Margaret Smith criticised Scottish Natural Heritage's (SNH) move.
Mr Finnie said the Highlands was an "appropriate" base for the agency.
The minister was asked why the Scottish Executive pressed ahead with the relocation against advice from the civil service and opposition to the move among members of staff.
Mr Finnie said the executive's policy on relocating jobs to other parts of Scotland was made on a case by case basis.
He said there have been instances where it had not been appropriate to take them out of Edinburgh.
However, he said while issues of natural heritage could be found throughout Scotland a "substantial proportion" were in the Highlands, making Inverness a suitable location for SNH.
Mr Finnie said: "It is certainly an area that is entirely appropriate for the location of that kind of enterprise."
Labour backbencher Ms Deacon highlighted the opposition to the move.
The Edinburgh East and Musselburgh MSP said: "The senior civil servants said don't do it, the chief executive and chairman of the board said don't do it, an independent report said don't do it.
"In those circumstances you decided to take full responsibility for a £21m expenditure of public money."
Mr Finnie said that he was aware of the opposition to the move to Inverness from SNH following a series of meetings with its board.
However, he added SNH's preferred option - staying in Edinburgh - was not "seriously an option" as it did not fit in with the relocation policy.
Liberal Democrat Edinburgh West MSP Margaret Smith said there had been "substantial losses of staff" with many SNH employees not transferring to Inverness.
Mr Finnie denied SNH had lost out on expertise by moving north.
Usually committee members quiz officials but they have decided on this step because the government over-ruled civil service advice.
The agency's move to its new home at Great Glen House was criticised by unions and MSPs.
First Minister Jack McConnell defended the policy of moving jobs out of Edinburgh as he opened SNH's new headquarters last year.
He said the move was good for jobs and devolution.
Unions said only 55 staff made the switch with 109 opting for redundancy. Great Glen House is also a base for the Deer Commission for Scotland.