Salford City Council demanded a judicial review following the news that it was downgraded from 'fair' to 'weak' just days before the final scores were published.
A spokesman said: 'As late as last Friday, Salford was led to believe it [would be] in the fair category - and this was apparently confirmed by a media leak last week in LGC.'
Leader Bill Hinds (Lab) called the score 'some kind of administrative sleight of hand'.
He continued: 'We believe we have been penalised as a result of some kind of paper exercise.'
Torbay Council, in the 'poor' category, was poised to take an injunction out against the Audit Commission to remove its name from the table. It has dropped this but is planning to seek a judicial review.
Bill Norman, Torbay's assistant chief executive, said: 'Unfortunately the CPA is irrationally simplistic in its judgments and based on a methodology that lacks transparency and objectivity.
'Having taken advice, it is also clear the assessment is without proper statutory foundation and should for this reason be challenged.'
Ealing LBC was downgraded from 'fair' to 'weak' at the last minute and its lawyers were in court seeking an injunction the day before the results came out. However, after the Audit Commission invoked its dispute resolution procedures and went to the council to discuss the score, they dropped the challenge.
An Ealing spokesman said: 'We were seeking an injunction over some last-minute changes and inconsistencies in our report. There are some minor changes in our corporate assessment which turned our score from 'fair' to 'weak'.