The website of the Symbiosis Institute of Media and Communication (SIMC) in Pune was hacked late on Sunday, and the homepage defaced with sentences in Arabic.
The hacker is believed to be a supporter of the Islamic State (ISIS), who had also reportedly hacked the website of Tsuingua University in China last week.
"The management was informed by a student after midnight on Sunday that the SIMC website had been hacked. We immediately contacted our vendor, and took down the site for a few hours," Vidya Yeravdekar, the Symbiosis education group's principal director, told IBTimes India.
"The vendor has informed the cyber-security cell of the police. We will be extra vigilant to ensure such incidents do not occur on our college websites again, especially since the admission season is on, but those who want to commit such acts can find their way to do it," she said.
Only the homepage of the SIMC website was defaced, Yeravdekar said.
According to DNA, the hacker had identified himself as "Don-2" and had posted threatening messages in Arabic.
A hacker with a similar name, who claimed to be an ISIS supporter, had broken into the Chinese university's website on 17 January and placed the image of an ISIS flag on the homepage.
The hacking of the Indian university's website comes amidst arrests of more than a dozen people for allegedly having links to the terror group.
Indian authorities are on high alert over possible terror threats during the 67th Republic Day on Tuesday.