Andy Wightman, a land reform expert, questioned whether the Trust, one of the country's largest landowners, was acting lawfully in seeking to profit from the sale of a house it did not build and does not own.
Helen Finan, a psychotherapist, wants to sell the house in Inveralligin, Wester Ross, which she has owned since her mother died two years ago. But she says strict criteria imposed by the Trust could cost her tens of thousands of pounds to meet.
She had moved back from London to nurse her mother, from whom she inherited the croft and the house her mother had built in 1987. Her mother had bought the croft land from the National Trust for Scotland (NTS) in 2009 and Ms Finan had taken the house out of crofting regulation.
But the conservation charity imposed restrictions on the house, the most significant being that it could be used only as the owner's main residence and not as a holiday home or holiday let.
Ms Finan applied to the Trust to waive the restrictions and it agreed to remove the residency condition because it reduced the property's market value. The asking price is £290,000 with the restriction.
However, NTS would receive 50% of the difference in the valuation of the house with or without the residency restriction.
Ms Finan said: "This could cost me a lot of money, tens of thousands of pounds."
Mr Wightman, author of Who Owns Scotland and who normally supports measures to keep people on the land, said it was unclear whether the residency requirement was lawful, under the Title Conditions (Scotland) Act 2003. This was designed to protect "architectural, historic of other (flora, fauna etc.) characteristic of the land."
He added: "The only reason the croft house is devalued is because of the conservation burden NTS imposed and, in exchange for waiving the burden, NTS wants to be paid a substantial sum of money.
"What characteristic of the land is preserved or protected for the benefit of the public by insisting the owner of the house shall use it as their main residence and for no other purpose? None.
"An absentee conservation landlord is seeking to impose its values and will on another property owner who stands to be disadvantaged as a consequence. Is this right?"
The NTS said it was pursuing the very causes Mr Wightman espoused. Terry Levinthal, its director of conservation services and projects, said Mr Wightman was an eloquent and tireless campaigner on land reform issues but, on this occasion, he had missed the point.
He said the property had a title condition preventing its use as a holiday home. The NTS could have insisted it remained but, instead, was negotiating with the owner in a pragmatic way.
He added: "We are unashamed in pursuing our fiduciary duties as a charity. If in the end, parties agree to pay the Trust to waive the title condition, all money received will be ploughed back into conservation activities in the kind of crofting communities Andy Wightman is so keen to protect."