Tests were cancelled for some 800 students in the southeastern city of Lyon after about 300 protesters formed a human chain at two sites of the Lyon 2 university, officials said.
In the southern port city of Marseille, meanwhile, police moved in to remove an estimated 60 to 80 students blocking access to the law and economy faculties of the Aix-Marseille University.
Shortly afterwards the protesting students were joined by about 30 rail and dockers' union activists as they squared off against police.
Officials suspended tests scheduled for roughly 700 students given the risk of "disturbing the public order".
Elsewhere on Monday, police evacuated protesters at a university in the western city of Rennes, an operation carried out "calmly and without any incidents," the school's president Olivier David said.
Exams had already been halted last week after blockades at universities in Arcueil, the Paris suburb where Nanterre university moved the exams following weeks of student occupations, and at Grenoble in the southern French Alps.
Dozens of sites have been fully or partially blocked or occupied since the beginning of the year to protest government plans for stricter entry requirements, a key element of President Emmanuel Macron's wide-ranging reform drive.
At present, anyone who graduates from high school is guaranteed a place at a public university, where admission fees are often limited to just a few hundred euros a year.
That has led to intense overcrowding at many universities as well as high dropout rates as the number of people graduating from high school has soared in recent decades, with 80 percent currently obtaining a diploma.
But many students view the government's plan for a more selective admissions process as an attack on France's longstanding promise of free education for all.
For the far-left students who dominate the sit-ins, the protests are about much more than education -- they have echoes of the momentous French university demonstrations which spurred a social revolution exactly 50 years ago, in May 1968.
The education ministry has vowed to ensure that year-end exams will take place despite the blockades.
Nanterre university still completely blocked
It said on Monday that the protests appeared to be winding down, with only Nanterre still completely blocked, compared with four universities at the height of the protests.
Paris 8 university in the suburb of Saint-Denis remains partly shut down, as do four other sites across France (Limoges, Marseille and two Sorbonne sites in Paris), which is "just half the number of two weeks ago," the ministry said.
Many students anxious to wrap up the year appear to be increasingly exasperated with the protests.
On Friday, many students scuffled with protesters while trying to force their way into the exam centre at Arcueil.