Both were in a tunnel at the site in Bure, about 138 miles (223 km) east of Paris, when part of a rock face collapsed, emergency officials said.
Workers were evacuated and an investigation is under way. There was no nuclear waste at the location at the time of the rock slide, officials said.
The facility is being tested to store radioactive waste deep underground.
France is heavily dependent on nuclear energy and the site is required to house the most dangerous material.
The underground repository scheme is due to begin in 2025 but is still awaiting the government's final decision.
A rock slide has killed one person and injured another at a site for nuclear waste in north-eastern France.