The alleged offending came when she was alone with him in his classroom and she told investigators the man had said it was their secret.
When police made further enquiries, others spoke out about what had happened to them.
Mr Dufty said much of the offending was masked as innocent fun under names such as "tickle torture" and "upside downies".
"What went on wasn't a game, wasn't a classroom activity. It went beyond that," he said.
"[His actions] were deliberate, they were indecent and the accused knew it."
When Child, Youth and Family joined the investigation later, another four young girls came forward alleging similar behaviour.
Defence lawyer Richard Earwaker said his client "absolutely denies" the offending.
He told the jury they would have to carefully assess the reliability and credibility of young witnesses, some of whom would be recalling events from three years ago.
"Were [his actions] actually indecent or has there been misinterpretation or overreaction?" Mr Earwaker asked.
The former student whose complaint was the catalyst for the initial investigation gave evidence this afternoon, telling the court about how the teacher would make her expose herself when they were in the classroom alone after school.
She said he tickled her "everywhere" when she sat on his lap and she believed the other children would be upset if they found out about the pair's "private time".
In a police interview played for the jury, she also described a shed at the school where another similar act took place.
The trial before Justice Mary Peters is expected to last three weeks.