Some residents have complained the constant humming was keeping them awake at night and others feared it could affect the value of their homes.
SSE was issued with a noise abatement notice by the Highland Council in February to tackle the low-frequency humming sound from the Wester Balblair sub-station.
This was after new equipment was installed as part of the upgrade of the controversial 137 mile Beauly-to-Denny powerline. The first section of the line between Beauly and Fort Augustus went live last year.
The company, which was initially sceptical about the level of noise, said it would place acoustic jackets around individual components and then install an acoustic barrier around the entire equipment.
SSE has now confirmed this will cost around £2.5 million to do.
Steve Byford, chairman of the local community council, said the high cost of repair was a problem of SSE's own making
Meanwhile another £1m is having to be spent on acoustic barriers for equipment associated with the power line near Fort Augustus.
David Gardner, SSE's transmissions director, admitted this week that the problem could tarnish the company's reputation.
He said: "It takes time to find solutions because of the complex nature of the problem, but we are taking this very seriously. It is difficult for me to have to try to manage and it is not good for our reputation."