The registrar of societies said in a gazette notice that the license of self-proclaimed pastor Paul Nthenge Mackenzie's Good News International Ministries was cancelled effective May 19.
Mackenzie is alleged to have incited his followers to starve to death in order to "meet Jesus" in a case that has deeply shocked Kenyans.
While starvation appears to be the main cause of death, some of the victims — including children — were strangled, beaten or suffocated, according to official autopsies.
Authorities also banned four other churches including the New Life Prayer Centre and Church headed by flamboyant televangelist Ezekiel Odero, who has been linked to Mackenzie.
Odero is under investigation on a raft of charges including murder, aiding suicide, radicalization and money laundering.
His arrest in April followed the discovery of human remains in Shakahola forest near the coastal town of Malindi, with police saying the bodies belonged to Mackenzie's followers.
While prosecutors have linked the two preachers, Odero was freed on bail in May while a court last week extended Mackenzie's detention for a further 47 days pending further investigation.
A largely Christian nation, Kenya has struggled to regulate unscrupulous churches and cults that dabble in criminality.
The grim discoveries in what has now been dubbed the "Shakahola forest massacre" prompted the government to flag the need for tighter control of fringe denominations in the country with a history of self-declared pastors and movements.
Previous efforts have been fiercely opposed as attempts to undermine constitutional guarantees for the division of church and state.
There are more than 4,000 churches registered in the East African country of 53 million people, according to government figures.
Many of them — headed by larger-than-life pastors — preach the so-called prosperity gospel, urging members
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