Around 700 striking teachers did not return their markings by Thursday night's deadline, representing “around 30,000 exam papers”, French Education Minister Jean-Michel Blanquer said.
Affected students, who are mostly in the areas of Creteil and Versailles near Paris and in the cities of Dijon and Toulouse, will receive provisional marks based on their performance results during the year.
Their final grade will be adjusted once the missing exams papers are returned.
Most of the 743,000 students who sat their exams this summer, known as the “bac”, got their final results on time.
Blanquer has slammed the strike and threatened to dock the pay of “teachers who have decided to play this game, which completely goes against the principles of public service”.
Protesting markers are trying to convince the government to reopen talks on an overhaul of the French baccalaureat from 2021, which will see more continuous assessment and less dependence on final exams.
French President Emmanuel Macron pledged to overhaul the qualification during his election campaign in 2017, saying it was failing to adequately prepare teenagers for university and the modern job market.
This year's exams have also been hit by the leak of a maths paper sat by around half of students.
Police arrested 21 people — including 19 high-school children — this week in Marseille and Paris after the paper was shared via text message and WhatsApp in June.
Seventeen of them have since been released.