The company was forced to install acoustic screens last year in an effort to reduce noise which residents nicknamed the “Beauly Buzz”.
But since mitigating that sound, residents in the Highland village are now complaining about a new noise.
SSE has launched another investigation, admitting the latest noise was at a difference frequency and different from the original buzz from the Wester Balblair sub-station next to Beauly.
It was built two years ago to feed electricity created from the growing number of renewable energy projects into the National Grid, via the controversial £600 million Beauly-Denny power line.
But locals complained of excessive low-frequency humming, claiming it was disturbing their sleep and stopping them from sitting in their gardens.
Last year Highland Council issued a noise abatement notice in February, directing SSE to resolve the continuous sound from the site.
Specialist acoustic jackets were made for noisy equipment and large green sound barriers have also been placed around other reactors.
In addition, a defective reactor was returned to the manufacturer in Italy for repair.
But Steve Byford, chairman of Kilmorack Community Council, said that while mitigation work had been completed, problems still remained.
He called on the energy company to enclose the sub-station within a building, adding: “It is intermittent. There is no regular pattern to it all. It is very noticeable. It is very disturbing.
“I know that transformers in other parts of the world are notoriously noise.
“Because of that, some of them are in completely enclosed acoustic buildings.”
An SSE spokeswoman admitted the new noise was intermittent and at a different frequency to the original buzz.
She said: “It isn’t the same noise. It was being masked by the initial noise which we have now mitigated. We are carrying out very different noise monitoring to specifically identify the source.
“We understand the noise is coming from somewhere within the sub-station but there may be external factors adding to it.
“We will be doing various tests and we will be testing different pieces of equipment to understand when the noise is increasing and what it is that is increasing it, and that will determine what mitigation is put in place.”
She claimed that enclosing the station could cause additional noise as there would be fans required to cool down the equipment.
Highland Council confirmed there had been new complaints about noise from the transformers. A spokeswoman said: “The noise abatement notice is currently on hold while significant mitigation works are carried out by SSE. Monitoring is ongoing.”