The report, made public Wednesday, was ordered following the highly publicized strip search of a 15-year-old girl at a Quebec City school in February.
The incident sparked outrage right across the country after the girl told a local paper she felt violated by the search after school officials suspected her of selling drugs.
Education Minister Francois Blais said Wednesday the practice will soon be banned.
"First, it's not acceptable because it's a kind of humiliation for people," Blais said. "And second, only because it's not really efficient."
Fabienne Bouchard, a former prosecutor and retired lawyer hired to conduct the probe, wrote a school that has serious grounds to believe a student is involved in drug trafficking should call police instead of carrying out the search itself.
"The recommendations are clear and the investigation was necessary to clarify the practice and to clarify the law around the practice," Blais said.
He added that schools and police will need to co-operate in the coming weeks to find a solution on how they should deal with drug trafficking.
The Quebec City school board at the centre of the controversy defended its actions and said it was only following government policy drafted in 2010 after consultation with provincial police and school board officials.
The school principal in question said the girl disrobed behind a curtain and that there had been no physical contact.
No drugs were found.
Family lawyer Francois-David Bernier maintained the high school misinterpreted government guidelines on searching students and humiliated his client.
Blais said authorities will revise those guidelines in the coming months to make the roles of all involved more clear.
That previous Quebec policy document cites a 1998 Supreme Court of Canada ruling that school searches were permitted practice providing they are "reasonable.''
The issue of strip searches was not specifically mentioned, but the guidelines noted the high court ruled students cannot expect a full protection of their privacy while in school.
Fallout over the incident also led to the resignation of former education minister Yves Bolduc.
Bolduc said in the legislature that a strip search was permitted under "strict'' guidelines and in a "respectful'' manner when student security is at issue.
But in the days that followed, Quebec Premier Philippe Couillard said there was "no question'' strip searches should not be allowed in Quebec schools, except under extreme circumstances.