"I have specifically said that social media incited violence against students from the northeast in Hyderabad and Karnataka. I have not said anything against journalists. My comments were misinterpreted," he said.
Shinde created controversy Sunday for allegedly threatening to "crush" the country's electronic media as he said a section of it was portraying the Congress party negatively.
Information and Broadcasting Minister Manish Tewari defended Shinde and the United Progressive Alliance (UPA) government, and accused opposition Aam Aadmi Party and the Bharatiya Janata Party of "hounding the media".
"The home minister has clarified his statement. UPA never believes in hounding a journalist or media house. We stand for the freedom of media and journalists, but the media needs to be responsible whether their critique is bordering on the sensational," Tewari said.
"You have a complete spectrum of intolerant people who believe that anybody who takes a critical view needs to be hounded, be it in the new media or the mainstream media," he added.
Meanwhile, the BJP lashed out at Shinde for his alleged remark and said his outburst was a result of losing people's support.
"You are the home minister of India, how could you talk like this? You are losing people's support because of your corruption, governance, insecurity. Don't blame the media for that," BJP's Ravi Shankar Prasad said.