Mehdi Masroor Biswas reportedly confessed to operating the ISIS-friendly @ShamiWitness account before it was recently shut down.
The 24-year-old was charged with waging a war or abetting the waging of war against powers friendly to India, police commissioner M.N. Reddi said.
He is also charged under prevention of unlawful activities and anti-cyber crime laws, Reddi said.
Biswas is expected to appear in court in 24 hours. If convicted, he could face up to 10 years in prison, according to the police official.
He described Biswas as an ISIS "sympathizer."
An electrical engineer by training, Biswas was working as an executive in a food company until this week, Reddi said.
The exposure this week in UK media of the identity of the man behind the prolific Twitter feed captured headlines worldwide.
The suspect told CNN's UK affiliate ITN that he expected to be arrested even though he believed he had done nothing wrong.
Fearing that the police might kill him during that operation, he also insisted to ITN that he would not resist arrest and was unarmed.
He said he had been overwhelmed by the frenzy of media attention since the identity behind @ShamiWitness was revealed.
"I thought it would die down within the first one or two hours but it's still raging. I can't believe this," he said.
Asked why he thought the persona had provoked such interest, he replied: "I think Shami Witness is the first person who really reached the people who like to wage war with the so-called war on terror.
