The Fiji Methodist Church says a submission to the iTaukei Affairs Ministry on the proposed village by-laws does not represent the views of the church.
In a statement, the Methodist Church said the submission had been drawn up by a sub-committee that went beyond its terms of reference and it made this point to the military's Land Forces commander on Thursday.
Earlier the military issued a statement raising concerns that a prominent religious organisation was talking about the supposed marginalisation and agitation of iTaukei.
It said this could heighten ethnic tensions.
The Methodist Church said the way the submission was prepared and sent out was a serious breach of its procedures.
The church said it remained committed to working with the government on key issues, such as climate change, gender-based violence, eduction and social welfare.
It said these are all part of Christian life and important pillars of the church.