Chief Minister Pinarayi Vijayan took the decision and directed the state Home Department to commence the proceedings 'as per rules' against Thomas, the senior most IPS officer in the state cadre, official sources here said.
He 'violated' the service conditions by not obtaining prior permission for his autobiography Sravukalkkoppam Neenthumpol (Swimming along with sharks). Besides, some of its contents were also violative of the service rules, the sources said.
The development comes nearly a month after a three-member committee, which went into the issue, submitted its report to the government.
The book also contained alleged adverse observations about certain Congress leaders and former ministers.
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"Sravukalkkoppam Neenthumpol" was to have been released by Chief Minister in May this year.
However, as a controversy erupted over some of its contents, Vijayan had kept away from the book release function at the last moment.
Thomas, who courted controversies during his tenure as the Vigilance Director, was on leave since April 1 this year following a direction in this regard from the chief minister.
On his bare-all autobiography in which he goes down memory lane over 30 years of his professional experience, Thomas had earlier said he paid the price for fighting corruption, but harboured no regrets.
Known for his strong stand against corruption, the IPS officer had earned the ruling CPI(M)'s ire after he registered a vigilance case against then industries minister E P Jayarajan over nepotism allegation following which he had to resign from the cabinet.
Chief secretary, K M Abraham and Additional chief secretary, Tom Jose, had lodged a complaint with the Chief Minister against Thomas after the Vigilance department conducted raids on their residences over alleged disproportionate assets.