Proposals by Scottish and Southern Energy Power Distribution (SSEPD) include building 50-metre high electricity pylons near to Culloden Battlefield.
In addition, the structures will be located near the 4,000-year-old Clava Cairns, Castle Fraser and Leith Hall.
The new route was suggested due to amendments being made to the preferred route during a consultation in 2015.
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However, in a letter to SSEPD, NTS Chief Executive Simon Skinner said research has shown overhead powerlines as "one of the most significant factors in degrading valued landscapes".
"It is therefore imperative that the careful siting and, where appropriate, undergrounding of power cables is followed," he said.
"It is unacceptable, for example, that in the case of Culloden, if this project goes ahead there will be no less than three large overhead lines passing through this glen within a mile or so of each other. This is not something we can support."
The NTS was one of the original objectors to the Beauly to Denny power line and has since expressed concern about its impact on wild landscapes, moves to incorporate new infrastructure and to make the access tracks used for its construction permanent.
"I completely understand that the country needs to upgrade its capacity to transmit electricity," Mr Skinner added.
"What disappoints me with this scheme is that SSE seems to be coming up with the cheapest, least imaginative and most damaging options possible."
(LM/MH)
