The deadly landslide occurred in an underground laboratory site at Bure in the Meuse department (see map below).
The two people involved in the incident were in a tunnel currently being dug at the site, a spokesman for the emergency services said.
Officials said no nuclear waste was at the site at the time of the incident.
Psychological counselling was offered to employees at the facility.
The site is managed by the National Agency for the Management of Nuclear Waste (Andra) and is designed to hold waste 500 metres underground, once it opens for use.
The project is still in a testing stage with scientists examining whether the most toxic nuclear waste could be contained safely underground.
Known as Cigeo, the project is still awaiting approval from the French parliament.
A bill is set to be presented this year with building work to begin due to begin in 2018 and the construction of storage facilities not scheduled to start until 2020.
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To appease locals, Andra is already spending €60 million ($80m) every year to support local community projects in the sparsely populated area.