Huge clouds of black smoke spewed into the air across north-western France as more than 5,000 tonnes of chemicals and oil burned at the site last week.
Authorities say tests carried out after the blaze at the Lubrizol plant indicated that the smoke was not toxic.
But environmental activists and unions accuse officials of "hiding the truth".
On Tuesday, several schools were closed after children said they felt nauseous and complained of sore throats and eyes, local media reported.
Later, hundreds of people marched through Rouen carrying placards that read "our children are in danger"; "assurances for pupils" and "it's up to us to investigate".
The march, organised by unions and activists, called on authorities to fully investigate the incident at the plant and to share the findings relating to any possible impacts on public health.
The plant belongs to Lubrizol, a US chemical manufacturer owned by billionaire investor Warren Buffett.
In a statement days after the blaze, Lubrizol said that CCTV footage and eyewitness accounts had suggested that the fire started outside the factory grounds.
"The origin of the fire [appears to be] external to Lubrizol and the fire unfortunately spread on to our site," the company said, adding that it was fully co-operating with the police.
Police have yet to confirm the cause of the fire.
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