Officials said they were investigating tax avoidance on the TV channel Bharat SamaChar and the Dainik Bhaskar newspaper.
Some employees have also been raided, and many have their cellphones seized.
Some media rights groups and opposition parliamentarians said this step was an intentional attack on press freedom.
But Anurag Thakur, Information and Minister of India Broadcasting, denied that the government was involved.
“The agency does their own work, we don’t interfere in its functions,” he said.
Dainik Bhaskar, published in Hindi, is one of the most read daily newspapers in India.
Throughout the state outbreak, paper and Bharat SamaChar have exposed the shortcomings in the government’s response to pandemics, including lack of oxygen and hospital beds.
They also reported on the body allegedly the victims of Koronavirus who had floated in the Ganges.
Why journalists in India are attacked
In April, Dainik Bhaskar published the Numbers of the Vaghani Phone Number – Gujarat State President who arranged the Bharatiya Janata Janata Party (BJP).
Recently reported the use of Spyware Pegasus NSO Group against several Indian journalists.
Responding to the raid, the two media outlets accused the government to intentionally target them for their coverage.
“RAID is the result of our aggressive reporting,” said Om Gaur, National Editor of Dainik Bhaskar, talked to Washington Post. “Unlike other media, we report how people are dying because of lack of oxygen and hospital beds.”
In a post on Twitter, Bharat SamaChar said: “The more you suffocate us, the harder we will tell the truth.”
Since the Prime Minister Narendra Modi in 2014, several media outlets have been investigated by the Government of Financial Inaccuracy, increasing concerns about the freedom of the press in the world’s largest democracy in the world.
In 2017 the tax authority stormed the NDTV broadcasting office, and its founder houses, Roy’s family.
Unlimited reporters, an advocacy group for journalists, has placed India in 142st position in the rank of press freedom – placing a country equivalent to Myanmar and Mexico.