Vijayan forwarded the report, submitted by Chief Secretary S.M. Vijayanand in December last, to the Director General of Prosecution for advice.
The report prepared by the Finance Department headed by Additional Chief Secretary K.M. Abraham suggested removal of Thomas from the present post.
Senior Indian Police Service officer Thomas, as Ports Director a few years ago, was accused of causing financial loss to the state.
After the Vigilance Department conducted searches at the residences of K.M. Abraham and Additional Chief Secretary Labour Tom Jose in 2016, IAS officers in Kerala are up in arms against Thomas.