Harbour assistant coach Scott Guthrie claimed he received a cut lip after being struck in the face by a notebook and pen wielded by Stewart before a pre-season game against Zingari-Richmond at Montecillo on Saturday.
Stewart, who coached University B last year before taking on the job at Harbour, told the Otago Daily Times yesterday he had stepped down from the head coaching role but had not been sacked.
He declined further comment.
Harbour club captain and coaching co-ordinator Jack Medder confirmed Stewart had resigned as coach of the premier side.
The club called an emergency meeting last night to discuss the incident.
Guthrie said, when contacted, Stewart had been grumbling over different things for several weeks and things came to a head on Saturday.
"We are struggling to understand what happened," Guthrie said.
Guthrie said Stewart had walked to the top of the ground, away from other coaches and club members, during the first of two games.
"As the second trial was starting he approached me and gave me a verbal spray. He then stuck his pen in his notebook and then pushed the notebook and pen into my face and cut my lip," Guthrie said.
"Everyone who was there was mystified by it. He then stood behind the posts for the rest of the game. Senior club members went up to him but he said he had had enough."
Stewart did not attend the after-match function.
Guthrie said he had known Stewart for years and he had no issue with him before.
"It was something I did not expect."
Guthrie, who said he was the new Harbour coach, said the change should not impact on the team, which beat Zingari-Richmond in the premier trial game.
Guthrie said he had a slightly swollen face but he would not press charges against Stewart.
He just wanted to get on with the season, which starts on Saturday.
Otago Rugby Football Union amateur rugby manager Justin Gardner said he had not heard of the incident.
The union would have to get all the facts and see whether it was within its jurisdiction before making a decision on whether it should investigate, Gardner said.