Sangma, whose outfit is fighting for a separate Garoland, was arrested July 30 near the India-Bangladesh border in Meghalaya. He was accused of waging a war against India.
He was presented before First Class Judicial Magistrate KM Lyngdoh Nongbri at the end of his police custody.
The investigators sought a 14-day extension in his police custody to question him over the kidnapping and extortion cases in Williamnagar, the district headquarters of East Garo Hills district, but the court rejected the plea.
Sangma, a former deputy superintendent of police, deserted the Meghalaya Police and floated the GNLA in November 2009.