Mr Vijayan, inaugurating the 2017-19 Delhi Union of the Kerala Union of Working Journalists (KUWJ), said that the RSS considered religious minorities as an "internal threat" to the country.
He also said that the RSS chief's allegation that the state government was supporting anti-national elements was a challenge to each Keralite and to Kerala society as a whole.
Mr Bhagwat, at a Vijayadashmi celebration in Nagpur in Maharashtra yesterday, had said that in the Left-ruled Kerala and the Mamata Banerjee-ruled West Bengal, "jihadi and anti- national" forces were at work and the governments there were not only indifferent but at times lending a helping hand to them to "appease" a section of the voters for "petty political interests".
Rejecting the RSS chief's remarks, the Kerala chief minister has said, "It is a known fact that communal forces play a major role in disturbing the political atmosphere of Kerala. But certain media houses hide this fact and blame the progressive movements and organisations of the state."
"The RSS chief has said that the state government was supporting anti-national elements that are perpetrating the violence. But we treat communal forces as communal forces, terrorists as terrorists and criminal acts as criminal acts.
"The gentleman and his organisation consider religious minorities as an internal threat to the country. This is the code of principle of RSS," the chief minister said, adding that his government and the Kerala society were in favour of protecting the minorities.
Mr Vijayan, who was in Delhi to attend the CPI(M) Politburo meeting, also took a dig at certain media houses.
"They say that Kerala is inhospitable and is a killing field. They also say that Kerala lacks press freedom and we kill political opponents. Those who have no idea about Kerala might believe this.
"Senior media persons from Delhi came to Kerala to cross-check these facts and they even tweeted that Kerala is completely different from what is being propagated in the national capital," Mr Vijayan said.
The Kerala chief minister also said that his government was providing and would continue to provide security to minorities in the state.
While referring to the death of Haryana-resident Junaid Khan on a train recently, Mr Vijayan said that communal forces have created such a situation in the country that just because they are Muslims, they can be attacked.
"Where are we heading? We don't agree with this. We don't support such acts," he said.
He also said that certain corporate-led media houses were trying to malign the image of Kerala.
"A recently-formed media house has been spreading derogatory statements against the state. This is against media ethics," Mr Vijayan added.
He also referred to the latest report on World Press Freedom Index in which India was ranked at 136 among 180 countries in the world press freedom rankings.
"The present media scenario of the country is worrisome. The report also says that extreme right-wing has imposed censorship on media. This is alarming," he said.
He also spoke about the killings of senior journalists Gauri Lankesh in Bengaluru and Shantanu Bhowmick in Agartala.
"It's the intolerance that we can see here," he said and asked the journalists from Kerala who are working here to act as "unofficial ambassadors of the state".
Later in a Facebook post, Mr Vijayan said, "In the freedom struggle, Keralites and the state have made memorable contributions. The RSS leader need not impart lessons on patriotism to Keralites."
Mr Vijayan alleged that in BJP-ruled states, murders in the name of cow protection and communal polarisation were being justified and efforts were being made to malign Kerala.
That will be a journey in the wrong direction, he said.
"However big the communal force is, if attempts are made to disrupt the lives of people, the LDF government will not compromise and will not show any leniency towards those who come in between the Constitution and its values," he added.