Cala Homes has expressed interest in building around 130 homes on the 11 hectares site adjacent to Chestnut Lane, to the north of Old Mains Farm.
However, the land acts as an important flood store for the nearby Craigdhu Burn, sparking concerns future residents would be faced with a serious flooding risk.
The council decided not to include the site as being suitable for housing in its latest development plan (LDP2), which is now being assessed by the Scottish Government .
This designation has been questioned by Cala Homes which stated to the Scottish Government's reporter: “We have accepted the flood risk position and designed the proposed layout accordingly.
"The layout presented takes into account the existing 1:200 year flood event risk area, with an uplift of 33 per cent for climate change related mitigation measures.
"With this in mind, we are the view that a development can take place here which manages the flood risk and makes a feature and opportunity of it.”
It now appears the government official tasked with assessing the plan is echoing Cala’s objection.
In correspondence with the council, case officer Mandy McComiskie wrote: “The council has concerns over this site with regard to flood risk together with a number of other concerns.
"The developer has responded to the council’s site assessment work in some detail.
"Given the particular circumstances and history of this site the reporter would invite the council to update its assessment of the site taking into account the submissions put forward by the site promoter, including but not limited to their more recent flood risk assessment.”
The council though has refused to change its mind.
It responded: ”Given the proximity to the on-site watercourse and scale of the proposal, the council has a number of significant concerns relating to the water environment.
”It is not considered reasonable or credible to state that development could make a feature and opportunity of flood risk.
"There is no justification to amend the current SEA conclusions or scoring.”
This has been backed by West Scotland list MSPs Pam Gosal and Ross Greer who have both urged the council to stand its ground.
Mr Greer said: “The LDP2 was approved by local councillors, is effective at protecting greenbelt land and already ensures that there is adequate provision to meet local housing and infrastructure needs.
"There is simply no compelling case for development of sites such as Old Mains Farm, and I support the council’s decision to resist any changes to the plan.”
Ms Gosal added: “With countless obstacles and little foresight, it is clear this development is a flood-risk and not in the best interests of Milngavie”.
“While I acknowledge the need for additional local housing, the potential for flooding is here is too serious. The developer has clearly not taken full account of the risks, or proposed adequate flood storage to tackle them.”