In his judgement, Justice S R Sen said the High Court will not interfere in the MPDA order of the district administration under which Sangma had been booked.
Sangma was booked under MPDA by the East Garo Hills district administration in January this year.
Today's order came as a blow to the GNLA chief as the High Court had last month set aside an MPDA order issued by the West Garo hills district administration, saying the authorities had failed to get the approval of the state government.
Sangma headed an armed militant outfit, the Garo National Liberation Army which is in operation in at least five Garo Hills districts in Meghalaya before he was detained in Bangladesh and pushed back to India last year where he was subsequently arrested and charged for waging war against the nation.
Sources close to the family of the jailed militant chief said that they would file an appeal with a higher court challenging the order.