The sites would be closed from April 16th to 20th inclusive but employees would be paid their full salaries during that period, Amazon said.
The CGT union told AFP the works committee had voted for closure of the sites for a total clean and evaluation of the risks.
Ealier this week a court in Nanterre, outside Paris, said Amazon France had “failed to recognise its obligations regarding the security and health of its workers,” according to a ruling seen by AFP.
While carrying out a health evaluation, Amazon can prepare and deliver only “food, hygiene and medical products,” the court said.
The injunction must be carried out within 24 hours, or Amazon France could face fines of one million euros ($1.1 million) per day.
Amazon were given one month to carry out the evaluation.
The ruling comes as consumers around the world flock to Amazon during the coronavirus lockdown.
But concern has grown over the safety precautions taken by the company, and dozens of workers protested in the United States last month.
Amazon has been hiring thousands of workers as business booms in countries affected by the coronavirus outbreak after authorities imposed business closures and stay-at-home orders to try to limit infections.
The company said Monday it had filled the 100,000 US jobs it promised a month ago to meet demand from the coronavirus outbreak, and was ready to take on 75,000 more.
But Amazon France's biggest labour union took the company to court saying more than 100 workers were being forced to work in close proximity despite the nationwide ban on public gatherings in force since mid-March.
Last month, French Finance Minister Bruno Le Maire accused Amazon of putting “unacceptable” pressure on employees after unions claimed the retailer was refusing to pay staff who did not go in to work for fear of coronavirus contagion.
His comments came after hundreds of employees walked out at several Amazon processing centres in France, exercising the “right of refusal” in France's labour code if an employee considers there is a risk to health or safety.
Amazon disputed claims that it was not taking sufficient precautionary measures, saying it had imposed stricter cleaning protocols and taken steps “so that employees can keep the necessary distance from one another.”