Those behind the legal action which prevented a new Madras College being built in 2016 have raised issues with the proposal for Langlands.
St Andrews Environmental Protection Association – Stepal – said it was “very pleased” with the new site west of Andrew Melville Hall but criticised the location of the building within the site.
Councillor Brian Thomson accused the group, which won an appeal to the Court of Session, of negativity.
He said: “It seems to me that Stepal is intent on fighting the battles of yesterday.”
However, Stepal insisted it had simply suggested refinements and hoped the school will be built as soon as possible.
Fife Council’s education service has lodged a planning application for the £50 million school which it is intended will be ready for the 2020/21 session.
Stepal has not objected to the proposal, which it said would improve community services and access to St Andrews University, but suggested the school would be better built in the north-east of the site to allow for future expansion.
This would also make it closer to the A91, where bus services are more frequent, and playing fields at Station Park, it said.
The submission states the site at Langlands is “immeasurably better” than Pipeland was but “there are some issues which can and should be addressed before the plan is finalised.”
Mr Thomson said: “Given that Stepal lists children and young people as a beneficiary of its activities, it is disappointing that yet again it has intervened in what can only be construed a negative and picky way with regard to the proposal for a new Madras College.
“Surely now is the time for an organisation like Stepal to get behind the exciting plans for the new Madras College, and warmly endorse them.”
Stepal directors said they had supported, endorsed and applauded the decision to build the school on the west side of St Andrews several times.
They said: “Our recent submission to the planners has stated strong support in principle, and also of the design of the school building.
“Our comments are therefore mostly positive with a couple of suggested refinements which would make better use of the chosen location.
“They take account of the fact that two-thirds of Madras pupils, along with parents, teachers and community users, some without cars, will have to travel to the school from the north and west along the A91, not just the third who come from the town and who are being well catered for by the school location and access within the town.
“These comments may or may not be accepted, but either way it will not change our strong approval of the project.
“Like most good-spirited and community-minded people in the Madras College catchment we wish the endeavour every success and with minimum further delay.”