Mr Naidu, who was the Information and Broadcasting Minister before getting elected as the Vice President, said he was "not pleased" with India's ranking in the World Press Freedom Index.
This issue should be addressed by strengthening media's independence, ensuring transparent flow of information, making legal framework more coherent and ensuring safety of journalists, he said.
India's World Press Freedom Index ranking plunged to 136 in 2017.
Mr Naidu, in his keynote address at the Ramnath Goenka Awards for Excellence in Journalism, also said that he twice expressed the desire before Prime Minister Narendra Modi to retire from active politics and devote his time for social work after turning 70.
Mr Naidu said the Prime Minister told him that he still has time to turn 70, which will be in 2019. He is 68 currently.
Recalling the days of emergency when he was a student leader and was jailed, Mr Naidu said the prison had all the necessary amenities but people inside were unhappy because of the confinement and craved for freedom.
"Journalism is all about conversation of the people and for the people. This is possible in an environment of freedom of expression. This freedom (of expression) should not be trampled upon as it was done during the emergency," the Vice President observed.
"We also need to understand the scope and nature of freedom of speech and expression. Can this be an absolute right? It cannot be absolute freedom. It comes around with certain responsibilities and restrictions," Mr Naidu said.
He said that the Constitution has imposed certain restrictions on freedom of speech and expression in the interest of sovereignty and integrity of India, public order, decency and morality.
The Vice President noted that in a democracy it is necessary for the "opposition to have its say and the government must have its way" and emphasised on debating, discussing and then deciding on issues.
Noting that the growth rate of the media and the entertainment industry from 2011-16 was 17 per cent, Mr Naidu cautioned that sensationalism and yellow journalism was the "dark side" of journalism which needs to be addressed.
He also rued that too much time was being spent by a section of media on trivial issues and advocated transparency and accountability.