Reverend Nigel Parker allegedly struck the seven-year-old boy in the face and on the hand.
Police were called in after the alleged assault happened on May 19.
Rev Parker was charged with assault and suspended from his duties at Bucksburn Stoneywood Church in Aberdeen.
A spokesman for the Church of Scotland yesterday confirmed that another minister was carrying out services there in the meantime.
He said: "Rev Nigel Parker has appeared in court and the case has been adjourned for trial until November 2013.
"I can confirm that Mr Parker has been placed under administrative suspension by the Presbytery of Aberdeen pending the outcome of any court proceedings.
"In the meantime, services at Bucksburn Stoneywood Church are continuing with a temporary replacement minister."
The minister is believed to have worked at the church on the outskirts of the city for a number of years.
He is one of 12 ministers of Aberdeen Presbytery who lodged an appeal against a decision by the presbytery to appoint gay minister Reverend Scott Rennie at Queen's Cross Church in 2009. Rev Rennie is believed to have attended the Bucksburn church as a youngster.
Rev Parker, who lives in the city, denies assaulting the child at Sclattie Park in Aberdeen on May 19.
The spokesman added: "It would be unhelpful to all concerned to make further comment while this matter is sub judice."
Rev Parker is due to go on trial at Aberdeen Sheriff Court.