France is one of few European nations to use so-called defence ball launchers, known by the French abbreviation LBDs, which shoot 40-millimeter rubber projectiles that are considered non-lethal.
French authorities “should suspend the use of LBDs during operations aimed at maintaining public order,” the council's human rights commissioner Dunja Mijatovic said in a statement.
She also urged the government to review its regulations soon on the use of so-called intermediate weapons for riot control, to ensure they respect law enforcement's primary task of protecting “citizens and their human rights.”
The reported injuries “raise questions about the compatibility of the methods used in operations aimed at maintaining public order with due regard for these rights,” Mijatovic said.
Police have used the rubber bullets extensively during the weekly “yellow vest” protests in Paris and other cities since November, which have often degenerated into clashes with police and vandalism.
Critics say they have caused severe injuries to dozens of protesters, including several who have been partially blinded after being struck in the head.
Mijatovic's recommendations follow a visit to Paris in January to evaluate the use of force by police, which many yellow vests say has provoked some of the violent responses by demonstrators.
French authorities have rejected the claims, saying both rubber bullets and stun grenades are required against violent individuals who mingle among the yellow vest activists who have repeatedly attacked security forces.
The country's top administrative court also ruled this month that the riot guns' use was justified given the sustained threat of violence.
On Saturday around 47,000 protesters again demonstrated across France against President Emmanuel Macron, accused of pursuing pro-business policies while ignoring the daily struggles of people in rural and small-town France.
In Toulouse, southern France, on Monday 14 protesters, with injuries including a broken jaw or a missing eye, filed complaints against the police charging “unprecedented police and judicial repression,” lawyer Claire Dujardin told a press conference.
The French government contested the council's findings, saying the guns were needed to suppress repeated attacks committed by a hard core of protesters against police officers, journalists and others.
“The impossibility of excluding such incidents in coming demonstrations requires the ability to use these weapons, which are particularly appropriate in these types of situations,” it said in a statement.
France was rocked by the images of scores of burning cars and ransacked businesses during the initial protests, when thousands of rioters staged running street battles with police in Paris.
Although the violence has subsided, sporadic clashes still erupt, including a shocking image of a former boxer bashing two riot police captured on video in January.
French lawmakers are now pushing through a bill that would let police ban known or suspected hooligans from demonstrating, and increase their powers to search potential demonstrators for weapons, without a prior court order.
The bill, expected to be finalised in March, would also ban demonstrators from masking their faces in order to avoid identification.
In her report Mijatovic warned the government that such measures “constitute serious interferences with the exercise of the freedom of movement and the freedoms of assembly and expression.”