The issue was discussed by Chief Minister Mukul Sangma during a meeting with senior administration officials to review law and order at Tura in West Garo Hills on Saturday.
Traders and government officials have been receiving extortion demands from small militant groups like Garo National Liberation Army (GNLA) and Liberation Achik Elite Force (LAEF), the officials said.
The mobile towers of the SIM cards from where the extortion SMS have originated were traced to states like Mizoram, Nagaland and Manipur.
"The militants have procured these SIMs from these states under fictitious names and producing fake identity cards," an official said.
The Chief Minister has asked the officials concerned to take up the matter with mobile operators at the highest level and ensure that the SIMs do not fall in hands of militants.
He also asked the authorities to find out from the cell phone companies as to how SIM cards land up with militants and miscreants.
The officials from Garo Hills were told to ask telecom operators and distributors to ask them to issue mobile phone connections only to those people who have valid addresses.
Police say some overground workers of the militant groups might also have procured distributorships from the mobile operators.
"The overground network of the militants is playing a big role in making the Garo hills belt of Meghalaya restive," police said.
There are an estimated 10 million mobile phone users in the Northeastern states and Jammu and Kashmir, with special set of rules already in place for pre-paid users in the region. Eighty per cent of the total mobile users in northeast use prepaid connections.
Since the later part of 2004, when pre-paid connections were re-introduced after they were lifted for some time, the license for pre-paid connections has been awarded on an annual basis in the northeastern region.