Speaking to the media here, Balan said that if the Governor seeks a clarification, the state government will surely reply.
"We have never questioned the Governor and in case, if it sounded like that, it pains us," said Balan.
Kerala Governor Khan said it was most unfortunate that the constitutional head of the state came to know about the CAA resolution through the newspapers.
The Kerala Chief Minister on Tuesday moved a resolution in the state Assembly demanding the scrapping of the controversial Citizenship Amendment Act (CAA).
Khan said that he has no problem with any divergent views be it on the CAA, NPR or NRC, all he cares about is that rules are followed as stipulated by the Constitution.
"I have no problem with the government, opposition, or anybody holding a different view on CAA, NPR or NRC. Everyone is free...," asserted the Governor. But he added that the Kerala government is in violation of the rules of the Assembly.
"If there are any apprehensions, the government will look into it and do the needful. There is no clash at all with the governor. If there is any difference of opinion with the Centre, then the Governor should be told and there is no need for any permission to be taken from him," said Balan.
However, the CPI-M party organ, Deshabhimani, in its editorial on Saturday was critical of the conduct of Khan.
( With inputs from IANS )