In a silent but powerful protest, Trinity Church members gave a thumbs-down to the current leadership by refusing to endorse the rector’s handpicked panel for the governing board.

Nearly 45 percent of ballots cast in last week’s election for board members contained forbidden “no” votes against nominees, according to one accounting. The ballots only asked voters to check a box in favor of a candidate.

But the directives of the embattled rector, the Rev. James Cooper, prevailed. All 22 candidates put forth by Cooper’s nominating committee won their seats.

Cooper has been under fire for his leadership of the historic church, which is considered the richest in the Anglican world, with some $1 billion in Manhattan real-estate holdings. Critics charge that the church doesn’t devote enough to charity and that Cooper favors grandiose expansion plans.