Authorities added there were no reported victims at this stage. The fire at the factory of Lubrizol - a company that makes specialty chemicals - had started around 0240 local time (0040 GMT).
Around 130 firefighters were currently tackling the blaze at the site, and a security cordon had been put in place, Reuters reported.
Besides Rouen, residents of 11 surrounding municipalities were asked to stay home, while schools in the area will remain closed.
"We have no evidence that there is a risk associated with fumes," said Interior Minister Christophe Castaner on RTL radio.
The fire at the factory of Lubrizol had started around 02:40 am CEST local time.
The factory, which makes oil additives, is classified as a SEVESO site, i.e. industrial establishments in the European Union where dangerous substances are used or stored in large quantities.
According to media reports, an acrid smell surrounded the site.