Mombasa Governor Hassan Joho has given Motrex Transporters Ltd seven days to mitigate the emission of poisonous clinker dust or risk closure.
The company is at the centre of a storm after at least 10 residents of Kikambodia Kikaangoni ghetto in Mikindani died of suspected clinker poisoning coming from the company.
At the same time, NEMA has warned Motrex's license will be revoked if it links the deaths to the clinker dust.
Meanwhile, a mega demonstration has been organised on Monday to force the management of Motrex to stop clinker storage.
Human rights activists Fredrick Ojiro who was a whistle-blower is leading the protests.
The company says it has rented its sheds to Corrugated Sheets Ltd who trade in clinker.
It denied causing deaths, sickness or suffering.
An air quality test sanctioned by NEMA has proven presence of clinker in the dust reaching the community.
Clinker is a nodular material produced during the production of cement.
It causes severe skin irritation, chemical burns as well as damage to human tissue.
On Friday, the Star exclusively reported the plight of residents who have for over eight years choked with the clinker dust.
It listed deaths and the sufferings of school-going children, mothers and the elderly.
The report triggered Joho's orders that were delivered by county secretary Francis Thoya.
"This problem has persisted for long. It seems they (Motrex) are doing some mitigations but this is coming a bit late. I'll be compelled to close operations in seven days if there is no report [on compliance]," Thoya said.
The CS said the company violated basic health standards.
"We shall not run away from responsibility. We must deal with it. We don’t want to be seen to be frustrating businessmen -- that is not our aim -- but we must safeguard against any negative effects of this operation has to human lives," he said.
Thoya said Motrex has failed to set up a medical camp notwithstanding knowing the dire effects of clinker poisoning.
The county official said they are investigating circumstances the company got operating license because its operations affect the community.
"I'm sorry to say but NEMA has contributed to some of the problems we are seeing to today," he said.
Nema has issued improvement orders and gave timeliness.
Motrex's annual Environmental Audit Report was submitted to NEMA January 12 and subsequent ground inspection done August 2.
NEMA orders followed: "Sprinkle water on the motor-able pathways within the yard at least three times day to contain dust generation and emission of fugitive dust."
It added: "Erect iron-sheet barrier of at least three-meter high over and above the existing boundary wall separating the factory and the community by the end of October 2018."
NEMA said entire fuel area be band and oil water separator installed within the drainage system.
This is aimed at mitigating against ground contamination and the deadline is September 2018.
"Seek and obtain an effluent discharge license from the Authority by end of October 2018," the order read in part.