The move prompted Samajwadi Party chief Akhilesh Yadav to take potshots as to whether Adityanath would himself sign the order withdrawing the case against himself.
"Will the chief minister himself order withdrawal of the case against him?" Yadav, a former chief minister, said.
Apart from Adityanath, who holds the home portfolio, Union Minister of State for Finance Shiv Pratap Shukla, Bharatiya Janata Party MLA Sheetal Pandey and 10 others were respondents in the case.
The case was filed at Gorakhpur's Pipiganj police station on May 27, 1995.
The Adityanath government's order to withdraw the case against the chief minister was issued last week, just a day before the Uttar Pradesh Criminal Law (Composition of Offences and Abatement of Trials) (Amendment) Bill, 2017 was tabled in the state assembly.
Before the bill was tabled, Adityanath told the House that 20,000 'politically-motivated' cases were filed across the state over protest demonstrations.
The amendment would bring to an end all such cases that were pending before magistrates till December 31, 2015, he said.
Gorakhpur Additional District Magistrate, City, Rajneesh Chandra told PTI that the order for filing an application seeking withdrawal of the case from the court had already been received.
The prosecutor has been instructed to file the application before the court concerned, he said.
Gorakhpur is Adityanath's home turf, and he represented the Lok Sabha constituency five terms before being appointed the chief minister earlier this year.
The case was pending in a Gorakhpur court which had earlier directed that non-bailable warrants (NBWs) be issued against the accused for non-appearance.
In May this year, shortly after Adityanath took over the reins of the state, his government told the Allahabad high court that he cannot be prosecuted in another case for allegedly making a hate speech that was alleged to have triggered communal riots in Gorakhpur in 2007.
The government refused to grant the mandatory sanction for his prosecution.
Adityanath, who was then the local MP, made the alleged hate speech following the killing of a Hindu youth in a clash between two groups during a Moharram procession.
He was arrested and spent 10 days in jail before being released on bail.
The sanction was needed to file a charge sheet against him under Indian Penal Code Section 153-A on the charge of promoting enmity between different groups on grounds of religion and caste, an offence punishable with imprisonment of up to five years.
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