Among the reasons for opposition outlined in its letter to the council, the diocese said there had been a "failure to consult with all interested parties" before the schools were identified for closure in September last year.
Diocesan director of education Jeff Williams said: "This process has been flawed from the start, as we have explained to councillors and officers multiple times."
"The reasons the council have given for school closures have been unclear, inconsistent and risk doing further damage to communities that have already been hit hard by these ill-informed plans," he added.
A spokesperson for the council confirmed it had recieved the letter, and would "digest its contents".
"Throughout the School Place Planning process, we have actively worked with all stakeholders to ensure everyone is involved in the future of School Place Planning on the island," the spokesperson added.
In January, the full council narrowly voted to oppose the cabinet's plans to close five schools on the island.
However, the ballot was non-binding and advisory, with the cabinet having the final say on 6 March.
The local authority, led by the Alliance Group, previously said it was seeking to address a significant decline in pupil numbers due to a falling birth rate, which is causing a financial strain on the council.
It said nearly there were 1,900 unfilled places in mainstream schools as of October 2023 and it projected that figure to rise to 3,056 by September 2027.
