However, Vijayan said the petition of Additional Chief Secretary (Finance) K M Abraham against Thomas for conducting a search in his house in connection with a case was of "serious nature" and it would be examined.
He made the statement in the Assembly while replying to a submission of opposition leader Ramesh Chennithala that the administration had come to a standstill in the state due to the fight between top bureaucrats.
The chief minister said there was no difference of opinion about the capability of Abraham and "that is why he is still continuing as Finance Secretary".
On the controversial inspection conducted at the house of Abraham, Vijayan said, "What happened here was the examination of allegations in a complaint."
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However, he said the government would also examine whether all procedures were followed while conducting such an examination at the house of a senior official.
But at the same time, Vijayan said Jacob Thomas is an official fir for the post of the Vigilance director. The "government did not have the feeling that he had done anything unbecoming of his position as the Vigilance director."
Vijayan also questioned the recent statement of CBI in
the high court that it was ready to probe the complaint that Thomas had indulged in a private teaching job and received pecuniary benefits while on leave.
"The forces that did not want Thomas to remain in the post were suspected to be behind this," he said.
The chief minister also dismissed the Congress-led UDF opposition's charge that serious infighting was on among civil servants in the state and the administration had come to a standstill.
Yesterday, a team of IAS officials, led by IAS Association president Tom Jose, met Chief Secretary M S Vijayanand and expressed dissatisfaction over the functioning of VACB Director.
They had said that certain actions of the director had demoralised civil servants.