AUGUSTA — A Superior Court judge has overturned a decision by the commissioner of the state’s Department of Environmental Protection concerning noise complaints against a Vinalhaven wind power project, saying the agency head’s action had no rational basis.

Maine Superior Court Justice Michaela Murphy’s ruling, issued Monday in Kennebec County Superior Court, criticized DEP Commissioner Patricia Aho for participating in the department’s handling of the Fox Islands Winds case.

Aho had worked for Pierce Atwood LLC before being appointed deputy DEP commissioner and then acting commissioner on June 20, 2011. Pierce Atwood represents Fox Islands Wind. She overrode the DEP staff and an outside consultant’s recommendation 10 days after she became acting commissioner.

“That issue, which could have been avoided, has created an enormous amount of mistrust by the [Fox Islands Wind] Neighbors as to whether their grievances can receive fair treatment by the commissioner and the department,” Murphy stated in the conclusion of her ruling.

The judge said Aho’s continued participation could be viewed as “antithetical to the common notions of impartiality which Maine citizens understandably expect from decision-makers in Maine agencies.”

Murphy reversed Aho’s June 30, 2011, ruling, which sharply limited the times when Fox Islands had to take action to reduce noise from its wind turbines. The judge said that there was no rational basis nor relevant evidence to justify Aho’s amended compliance order that simply limited noise reduction requirements when there were the same weather conditions as the two days (July 17, 18, 2010) that the turbines were found to have exceeded the state’s noise limit (45 decibels at night).

Murphy ordered the matter remanded to the DEP for the issuance of a complaint compliance order that would be consistent with the findings of an expert that the department had hired but whose recommendation was overridden by Aho.

The three nearly 400-foot tall wind turbines were erected in 2009 with a dedication ceremony in November of that year. The $14.5 million project gained approval of island voters in July 2008. The project’s aim was to reduce electricity costs on the island and rely more on renewable energy.

At the dedication ceremony, neighbors voiced concern about noise that was being generated by the spinning turbines.

In September 2010, a consultant working for the DEP found that the wind power project was exceeding noise standards under certain weather conditions and should be changed to lower the noise. The DEP staff initially ordered Fox Islands Wind in November 2010 to change the way it operates to reduce the noise, but Aho overruled that order in June, shortly after she became commissioner.

Neighbors filed their complaint in July 2011.

Attorney Rufus Brown, who represents the neighbors, said Thursday the judge’s ruling does not mean that the Fox Islands turbines will cease to operate, but the DEP must modify its order on how the project must comply with noise limits.

He said the noise negatively affects the health of people who live near the turbines.

Emails were sent to several DEP officials on Thursday evening but were not immediately returned. Telephone messages were left Friday morning for Aho and Fox Island Electric representatives.