The interior minister, meanwhile, asked protest organisers to throw out members of far-right organisations who have been involved in the violence, as opposition intensifies ahead of the bill's expected final approval.
"Homophobic acts, violent acts have been committed. The right to protest is recognised by our constitution and accepted by the French. But no protest must degenerate," Hollande said.
The landmark bill -- which would also legalise adoption by gay couples -- was approved by the upper house Senate last week after being voted through the lower house National Assembly earlier this year.
It has now gone back to the assembly for a second reading, and could face a final vote as early as next Tuesday, under a fast-track measure that has limited debate to 25 hours.
Opponents have accused the government of rushing the bill through its final stages in the legislative process, and have upped the ante with daily protests.
On Wednesday, a several-thousand-strong protest in the streets of Paris turned ugly with cars and public property vandalised and police officers and two journalists attacked. Several people were detained for questioning.
The journalists from France's parliamentary television channel were "violently tackled and their equipment destroyed", the broadcaster, LCP Assemblee Nationale, said in a statement, adding that it would file a complaint.
In Lille, three employees of a gay bar were injured late Wednesday in an attack by four men who smashed the building's windows. The owner linked the incident to "tensions" over the parliament vote.
Politicians have also been targeted. Socialist lawmaker Sylviane Bulteau, who supports the bill, said she received a letter containing threats to kidnap her and to blow her up.
Protests against the bill have also taken place in Versailles near Paris, as well as the southwestern city of Toulouse.
Interior Minister Manuel Valls denounced the current climate in France as "sickening" after meeting with police representatives to reinforce security measures surrounding protests and to try to prevent homophobic assaults.
He warned protest organisers to beware of "hate speech" and asked them to "reject far-right groups", ahead of a large demonstration against the bill planned on Sunday.
Jean-Francois Cope, the head of the opposition right-wing UMP party, condemned the homophobic acts but said Hollande, "by refusing to listen to French people's concerns", was partly to blame for "deep divisions" in society over the bill.
Meanwhile, debate in the lower house turned sour as pro- and anti-bill politicians traded barbs, with Justice Minister Christiane Taubira likening the situation to "a bad Spaghetti Western", while one member of parliament said the proposed law equated to "killing children".
"What you are doing is (opening) a breach that will not close if this legal text passes through, it's an ignominy," said Philippe Cochet, a UMP member.
"You are killing children", he added, provoking an uproar that forced the speaker of the house to interrupt the session.
When the members of parliament returned, Cochet said the term he used was "not appropriate", but added that he still believed the bill would make children more vulnerable.