The youth identified as Rimialson Daw (26) was arrested from Baghmara in South Garo hills district, they said.
"We have arrested the youth after tracking the phone number and the services he used and 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 based on an FIR filed by the lone lady city legislator who alleged that Daw had sent her three hate sms on her mobile phone on the intervening night of 26-27 while she was returning back from the goodwill trip to states affected by the mass exodus of NE students.