The company at Elur, near Kochi, had persistently violated rules laid down to check air and water pollution and environmental hazards, PCB Chairman K Sajeevan said.
The undertaking did not remove stocks of Endosulfan and other hazardous chemicals at its disposal despite the Board enforcing a ban on its manufacture and sale about a year back, he said.
"We have given sufficient time to take steps on these matters. Again and again, the company authorities have been told about the violation of rules. But they chose to ignore them," Sajeevan said.
He said the Board had some time back asked an experts' team to look into the matter and the order to close down the factory was taken on the basis of its report.
Kerala has been at the forefront of a campaign demanding nationwide ban on Endosulfan as its use has allegedly caused large number of deaths and serious health problems to hundreds in Kasargode district.
Chief Minister V S Achuthanandan has himself spearheaded the campaign and undertook a day's fast recently seeking a nationwide ban on the pesticide and has written to his counterparts in other states asking them for their support.
CPIM-led LDF had also organised a statewide hartal a few days ago on the issue.