The youth, identified as Rimialson Daw, was arrested from Baghmara in South Garo hills district.
"We have arrested the youth after tracking the phone number and the services he used. He would be brought to Shillong tomorrow," East Khasi SP M Kharkrang told PTI.
According to the district police chief, Daw is working as a pharmacist at one of the government-run community health centre in the remote Garo Hills district.
Daw was arrested after the Urban Affairs Minister, who in her FIR, alleged that the youth had sent her three hate SMSes on the intervening night of August 26-27 while she was returning back from the goodwill trip to states affected by the mass exodus of Northeast students.