"We do not have a plan to shut down any of these platforms," Joe Mucheru, the minister for information, communication and technology, told Reuters. "Press freedom is one we cherish, whether it is (traditional) media or social media."
His statement echoed that of the interior minister, Fred Matiangi, who accused the NCIC of making haphazard decisions over the weekend, and vowed that the platform will not be shut down.
"They (NCIC) should have consulted widely because they don't have the power to shut anybody down. They don't license anybody," Mucheru said.
When it issued its ultimatum, the NCIC said it was consulting with the Communication Authority of Kenya, which regulates the industry, adding that it would recommend suspension of Facebook's operations if it does not comply.
The National Cohesion and Integration Commission (NCIC) on Friday accused Facebook of contravening Kenya's constitution and laws for failing to tackle hate speech and incitement on the platform ahead of Aug. 9 national elections.
Meta has taken "extensive steps" to weed out hate speech and inflammatory content, and it is intensifying those efforts ahead of the election, a company spokesperson told Reuters.
Supporters of the leading presidential candidates, veteran opposition leader Raila Odinga and deputy president William Ruto, have used social media platforms to praise their candidates, persuade others to join them or to accuse opposing sides of various misdeeds.
Kenya's presidential and other major elections take place August 9.