The council said the site directly behind St Clement’s was ruled out mainly due to Scottish Environment Protection Agency (Sepa) flood risk criteria.
A spokeswoman said: “Sepa classifies flood risk depending on the proposed land use.
“Schools are classified in the most vulnerable category and therefore certain types of land that are deemed unsuitable for school builds can be developed for other uses that fall into a less vulnerable category.”
The Scottish government said it was local authorities’ statutory responsibility to manage and maintain their school estates.
A spokesperson said: “Scottish government investment is intended to supplement this, not replace it.
“Phase three of LEIP supports a priority project in those local authorities who have not yet benefited from LEIP and, therefore, treats all councils fairly and equitably.
“Highland Council is receiving financial support from phases one and two of LEIP for the Broadford Primary School, Nairn Academy and Tain 3-18 Campus projects.”
The spokesperson said Education Secretary Jenny Gilruth had received the council’s letter asking for further engagement and would respond in due course.
