The officers wanted to proceed on leave to protest against what they said was Vigilance chief Jacob Thomas's "vindictive attitude".
After meeting a delegation of eight top IAS officials on Monday, Vijayan told the media that the government had taken a serious view of the protest.
"Such a thing is happening for the first time in Kerala and the way they went about taking leave can be termed a 'strike'. We view this very seriously," the Chief Minister said.
The Indian Administrative Service (IAS) Officers Association took the leave decision on Saturday after Thomas, who holds the rank of Director General of Police, indicted senior IAS officials in vigilance cases.
The latest to come under the scanner was Additional Chief Secretary Paul Antony, who has been named the third accused in the appointment of a nephew of then Industries Minister E.P. Jayarajan to a government job. An outrage sparked by the appointment led to the minister's resignation.
Vijayan said the immediate action which prompted the IAS officers to go on "strike" was the ongoing probe against some officials.
"This is a probe against some IAS officials. It has happened earlier where in certain cases officials have been suspended.
"I have made it very clear to them that their justification for the 'leave' is not legitimate," added Vijayan.
"The people who are supposed to run the government but resorting to this sort of action is not good. The officials said they have nothing against the state government," Vijayan said.
Asked if the IAS officials had submitted a complaint against Thomas, Vijayan said no complaint had been received.
"There were some cases against Thomas, of which some were cleared by the state government and some by the courts. Right now, there is only one case that is going on," he said.