Council chiefs said the proposals, for Newton Mearns, south of Glasgow, had created a significant public response and that it was being abandoned, in part, due to criticism of the move.
A report on wider proposals for the East Renfrewshire area, which is expected to be agreed next week, says: "In view of the volume of representations received, the sensitivity concerning the proposal and the extremely wide range of issues raised, it is recommended that this proposed modification be pursued no further and is not included in the plan."
The proposals for the mosque had been put forward by the local Muslim community as there is no permanent place of worship for Muslims in Newton Mearns, despite demand for more than a decade. The Muslim community had suggested a residual parcel of land next to the new Eastwood High School was its preferred site for a religious and community facility.
The Scottish Government's Reporter, who adjudicates on planning issues, has recently been critical of the length of time it has taken local Muslims to secure a permanent place of worship in the area and allowed temporary change of use of a former nearby British Legion club for Muslim prayer services.
An alternative location north of Newton Mearns has now been recommended, but another suggestion would be dependent on wider development plans.
Proposing the plans, Nazir Ahmed, a trustee of the East Renfrewshire Mosque and Community Centre group, said the East Renfrewshire Muslim community had been resident for more than 40 years and is "one of the fastest growing communities that actively contributes to the vibrant and ethnically authentic nature" of the area.
But the Eastwood High mosque plans sparked an opposition campaign, with parents complaining about a religious facility being built on non-denominational school grounds.
Parents said they had concerns at the possibility of violent protests outside the school gates and the potential for vandalism, fireraising or even terrorist- style bomb attacks following interest in the proposal from far-right extremists.
There had also been a political divide in the area, with support from Labour, while the SNP and Tories took the view "it was the right plan in the wrong place".
The report adds: "The identification of a suitable site for a Muslim religious facility remains a key aspiration of the council and the need for such a facility was supported by the wider community during the consultation process."
SNP councillor Vincent Waters said: "It's been disappointing to see so much negativity in the public discussion about the proposal."
Ken Macintosh MSP said: "This has been a genuine process which has addressed the concerns of parents and the upside is attempts to create racial tensions have entirely failed. I believe local residents will now unite to support the Muslim community to find a more suitable site."
A statement from East Renfrewshire Mosque and Community Centre said: "Muslims have been living in East Renfrewshire for over 40 years and have been trying to establish a mosque within the area for a number of years, without success.
"At present there a few community centres available which provide Muslim facilities to pray, but there is still no dedicated mosque for the growing Muslim community of East Renfrewshire.
"This is particularly unfortunate considering that East Renfrew-shire is a multi- faith and diverse community where there are numerous churches and synagogues."