Launched on Monday, the operation aimed to collect 527 samples from students and staff at Fenelon-Notre Dame, a private Catholic high school in the port city of La Rochelle, on France's Atlantic coast.
Authorities said that only about 20 samples remained to be taken today as part of the investigation into the rape of a 16-year-old girl on the premises in September.
The samples were to be analysed within a month and compared with DNA taken from the clothing of the girl, who was raped in a school toilet where the lights had been turned off.
Only one student refused, with local prosecutor Isabelle Pagenelle saying he had done so for "personal reasons" and had a "philosophical" opposition to giving a sample. The student was over 18.
Pagenelle had earlier warned that anyone refusing to provide a sample could be considered a suspect and arrested.
The procedure raised concerns, with critics arguing that individuals should have the right to refuse to provide DNA samples without being considered suspects.
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