It is hoped the Shell Pernis refinery in Rotterdam will be back up and running "at the earliest in the second half of August," a Shell spokesman told AFP.
Most of the units on the site have been closed since Monday "for security measures" after the pre-dawn fire broke out overnight Saturday to Sunday, the company added in a statement.
The refinery covers an area equivalent to 800 football pitches, and its pipework, if laid end to end, would be long enough to circle the Earth four times.
Firefighters brought the blaze under control in the early hours of Sunday. Shell has not confirmed media reports that the fire was started by a short circuit.
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But a second incident occurred Monday during the cleaning of one of the factories when there was a leak of a colourless, highly reactive gas, hydrogen fluoride.
"The source of the leak was detected and it was staunched," the company said. Both the fire and the leak are now being investigated.
"We expect to restart our operations at the earliest in the second half of August," the Shell spokesman added.
"We regret the impact this may cause for our customers, and we are doing everything we can to minimise impact to our customers," he added, asking not to be named, and also refusing to comment on whether there would be any impact on the oil markets.
The refinery has now ceased flaring off stocks of gas as part of the safety procedures taken during a shutdown.
There will be a new "flareoff when the site is relaunched," Shell said, adding it would seek to "limit any inconvenience" to those nearby.