Reverend Nigel Parker was claimed to have struck a seven-year-old boy's face and hand earlier this year. Police were called in after the alleged offence was reported on May 19.
The minister of Stoneywood Church in the Bucksburn area of Aberdeen denied the offence. He was suspended from his duties at the church and was due to go on trial at the city's sheriff court next month.
Yesterday it emerged the case against him had been deserted by the Crown.
A Church of Scotland spokesman said Rev Parker remained suspended. He said: "Under Church law the church has a process to follow before it can close the matter. It has not considered anything at this time."
Reverend Parker declined to comment on the case.