The commission says the charter, which has not yet been tabled in the legislature, contravenes a more fundamental law: Quebec's Charter of Human Rights and Freedoms.
Commission chairman Jacques Fremont says the plan is cause for concern and is a clear break with the text of the charter of rights, which was adopted in 1975.
"It is the most radical proposal modifying the Charter since its adoption," Fremont said Thursday.
Bernard Drainville, the cabinet minister responsible for the proposed charter, said Quebecers don't want the status quo said the commission "does not share the same understanding of the situation in Quebec" as the government.
"The commission said, 'Do not change anything. it's not necessary to be specific.' We say the opposite. It must be clarified."
That's a shift in attitude from last year, when Drainville used the commission as a reference point when attacking the Charest Liberals' anti-protest law.
While Drainville said Thursday that he respected the opinion of the commission, Drainville said the legal basis of the proposed charter had been validated by a number of eminent jurists, including former Supreme Court justice Claire L'Heureux-Dube.
Drainville said the commission failed to take into account that the government intends to enshrine secularism and the religious neutrality of the state in the Charter of Human Rights and Freedoms.
"The conclusions drawn by the commission are from the current charter," he said in an interview. "It's as if the commission didn't take into account the changes we want to make to it."
The values charter has set off a firestorm of debate since first being floated by the Parti Quebecois in last year's provincial election campaign.
There have been numerous reports of insults against Muslims, some of which have filtered into more mainstream media.
Popular Quebec actress Denise Filiatrault, in a radio interview this week, referred to women who wear a veils as "fools" and insulted those who cover their hair while wearing makeup.
Tabloid media have also been drawing attention to the method of slaughtering animals on farms for Ramadan celebrations — prompting one provincial minister this week to suggest there could be criminal charges for animal cruelty.
Meanwhile, opponents of the charter have held several demonstrations and another is planned for this weekend.
Court challenges have also been threatened and the federal government has said it will look closely at the charter if it ever becomes law.
Public opinion polls suggest there's fair support for the charter, which would ban workers in the public service from wearing obvious religious symbols such as hijabs.
Fremont said in an interview that complaints about religious symbols comprise a miniscule percentage of those received by the commission and he doesn't see any crisis that would require such legislation.
"The problems around this are negligible compared to the problems of reasonable accommodation for notably handicapped people and the elderly," he said.
"There are hundreds of those complaints every year, hundreds of cases."
Fremont suggested such a law as the values charter would probably do more to complicate life than simplify it.
It says formalizing religious accommodation could end up leading to restrictions on accommodations granted to others, such as the physically challenged.
The commission also questioned the government's contention that it is trying to provide protection against gender discrimination, saying that already exists in the charter of rights.
Quebec Liberal Leader Philippe Couillard welcomed the commission's statement and said he hoped it would prompt the government to reconsider its position.
"It's a considerable snub to the government," Couillard said of the commission's report.
Couillard lamented the downturn in the quality of the public debate over the charter, noting the comments by Filiatrault.
"This sort of slip, which borders on insult, certainly doesn't doesn't advance the debate," Couillard said.
Quebec Agriculture Minister Francois Gendron has also been quoted in media reports as saying he isn't ruling out criminal charges if an investigation into the ritual slaughter of sheep for a Mulsim religious holiday marking the end of Ramadan.
Gendron said inspectors are determining if there was any cruelty to animals and that carcasses were disposed of properly.
(With a file from Lise Millette)