The accused, whose name has been withheld by the agency, is a resident of Parbhani in Marathwada region of Maharashtra.
As per the press release issued by ATS, the man had been in touch with a person named Farukh, a resident of Syria and an alleged member of the Islamic State, through social networking sites.
The accused had created several IDs to remain in touch with Farukh, it said.
He has been booked under relevant sections of IPC and Unlawful Activities Prevention Act (UAPA), it added.
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In May 2014, four youths from Kalyan near Mumbai, namely Shaheen Tanki, Fahad Shaikh, Aman Tandel and Arif Majeed had left the country to visit holy places in the West Asia, but they disappeared thereafter and since then were suspected to have joined IS.
In December last year, four youths had disappeared from Malwani area--a western suburb of Mumbai--reportedly to join the IS.
While two youths, Noor Mohammed and Wajid Sheikh, returned to their homes, the whereabouts of Mohsin Sayyed and Ayaz Sultan are not known.