Warjri, the first woman home minister, submitted her resignation to chief minister Mukul Sangma late Thursday.
"I have resigned owning moral responsibility for the prevailing law and order situation in Garo Hills where precious lives of both civilians and men in uniform have been lost," Warjri said.
However, it is not known if the chief minister has accepted Warjri's resignation.
There have been a series of explosion in Garo Hills perpetrated by the Garo National Liberation Army (GNLA), killing two policemen and injuring three others.
The militant outfit had also tossed a crude bomb at a police outpost at Rongram in West Garo Hills. However, there were no casualties.
Warjri's comes ahead of the winter assembly session beginning from Friday where the combined opposition of Meghalaya People's Front (MPF) is planning to nail the government on criminalisation of politics, and total collapse of governance which led to deaths of civilians and security forces besides infiltration of militants into Meghalaya Police.