The Kirk's Church and Society Council and the Humanist Society of Scotland have proposed to MSPs that "religious observance" should be changed to "time for reflection". They said changing the legal definition could ease the concerns of parents who withdraw their children from them.
But Lewis Presbytery, the collective of the island's Church of Scotland congregations, said it wished to disassociate itself completely from the move.
The law requires religious observance, such as assemblies, in schools. However, since a change in Government guidelines in 2005, assemblies must be aimed at children of all faiths and none.
A Kirk spokesman said: "We note the comments from Lewis Presbytery and know they will note that this proposal will be looked at by the Church's highest court."