Ezekiel Odero now claims the decision to close his church is politically motivated and unreasonable.
In his case at the High Court, Odero argues that the Registrar of Societies failed to accord him reasonable time to file his annual returns.
He says the New Life Prayer Centre file has been missing and his efforts to trace it at the Registrar's office have been futile.
He claims that the directive was meant to beat the orders issued by Mombasa High Court judge Olga Sewe to re-open his church.
According to his lawyers Danstan Omari and Shadrack Wambui, the government is hell-bent to nail him without sin.
They maintained the alleged arrests over Shakahola deaths, the decision by the Communication Authority of Kenya and now the Registrar of Societies are an injustice to Odera and a violation of his followers' right to worship.
"It is increasingly disheartening of the numerous attempts by states organ to persecute me, frustrate my ministry and eventually not only shut down the New Life Prayer Centre and Church but also all my other projects," Odero states in his court papers.
He claims that the Registrar served him with a letter on May 25, 2023, indicating that the church would be closed if he failed to comply with the requirement to update his returns from 2012 to 2022.
The pastor, however, claims that the letter was backdated to April 27, 2023.
He asserts that it is unfair for the Registrar to require him to act on a timeline that has already lapsed.
"Unless this honourable court moves with celerity and arrests the impending illegality and injustices that are to be occasioned by the first respondent, the applicant shall suffer irreparable harm and his congregants' freedom of religion shall be curtailed in contravention of Article 32 of the Constitution," the lawyers argue.
He wants the court to quash the Registrar's letter and order the office to make available the church's file and pay costs of the case. He has also sued Attorney General.
"It's absolutely irrational for the first respondent to threaten to cancel the registration of New Life Prayer Centre and Church for failure to files its annual returns while being fully aware of the impediments it has tactfully placed to ensure that the applicant is unable to fulfil the church's annual returns without the church's file that is primarily in the first respondent's custody."
