Rev Sandi McGill, 53, of Avonbridge and Torphichen parish in West Lothian, has been removed from her post while Church of Scotland officials investigate.
Parishioners were informed of the suspension during a Sunday service. Rev McGill was only inducted at Avonbridge and Torphichen in July 2012, but her leadership style is believed to have antagonised some of the church elders.
However, other members of her congregation said Rev McGill had been targeted by church elders when she tried to introduce changes. The parish website describes Rev McGill as a "people person" who will "always make time for any who need her".
Rev McGill declined to comment.
A Church of Scotland spokesman said: "There is an ongoing inquiry by presbytery."