Chris Procunier said Wednesday that his wife Jennifer saw impressions from the tape on the boy's mouth after the alleged incident last Thursday afternoon.
His son was one of 11 students participating in the Excel after-school program at Bedford South School at the time, Procunier said in an interview.
Procunier believes he and other parents should have been informed immediately, even though students weren't in school Friday because it was a professional development day.
"Our biggest issue is the lack of response from either the school board or the Excel program. There's been no indication this is being dealt with properly," he said.
"If our kids hadn't told us this was happening, we wouldn't have known."
Procunier said he and his wife heard from three other parents last week that nine other children and their son were lined up for disciplinary action and had the tape placed over their mouths.
"My son said they were speaking out loud, but I'm not sure what the catalyst was ... and there was actual duct tape placed on the kids mouths for an extended period of time," said the father.
Procunier said he is upset the school only called him to a meeting on Tuesday where he, eight children, other parents, an Excel official and the school principal discussed what happened.
He said he wasn't satisfied after the meeting that the board had a clear enough set of policies to prevent other occurrences in the after-school program.
In a news release, Education Minister Ramona Jennex says she is "very upset" about the allegation and the department will work with the school board to ensure it doesn't happen again.
It is not clear from official sources how many children allegedly had their mouths taped shut. The provincial government news release refers to one child.
"Our schools need to be safe havens for children in this province," said Jennex. "I expect the school board to have answers about this alleged incident shortly and we will work with the board to ensure it doesn't happen again."
Police have confirmed they are investigating a report of an assault on Thursday afternoon involving a student and staff member at the school.
Doug Hadley, a spokesman for the Halifax Regional School Board, said the board is also investigating but he wouldn't say how many children were alleged to have had their mouths taped.
"At this point, we believe there was between 10 to 12 kids in the room but I can't confirm if the incident involved one, several or all," he said in an email.
He said some parents were contacted Friday or over the weekend, but others weren't informed until Tuesday.
The employee, who is an assistant instructor in the program, was immediately placed on paid leave until the board concludes an investigation on whether its policies were violated, Hadley said.
If it is shown that tape was used, Hadley said it would be a violation of board policies.
"We don't know what kind of tape was used," he said. "But regardless of that, it's the kind of action that should never occur under any circumstance."
Hadley said it's possible the board will review and amend its policies, adding that if the allegation proves true a policy review is likely.
"I would suggest to any of the parents that if they left the meeting not feeling satisfied, that they contact the Excel staff or board staff to express those concerns so we can take that into consideration," he said.