The decision, under which the controversial Armed Forces Special Powers Act (AFSPA) 1958 was imposed, was taken at a cabinet meeting chaired by Chief Minister Okram Ibobi Singh on Monday night.
"The cabinet has decided to extend the disturbed area status in all parts of Manipur, except in Imphal Municipal areas, based on reports submitted by security agencies," a government official said.
In the last few months, rebel groups have triggered over 30 blasts, killing and injuring security forces and civilians.
There are more than 20 rebel groups active in Manipur, a state bordering Myanmar, with demands ranging from secession to greater autonomy.
The Manipur government had lifted the controversial AFSPA in the seven assembly constituencies two years ago.
Manipur was declared a disturbed area in September 1980.
Besides Manipur, the AFSPA is also in force in Tripura (excluding the Imphal Municipal Council area), Assam and Nagaland, and in the Tirap and Changlang districts of Arunachal Pradesh.
Irom Sharmila Chanu, a human rights activist, has been on an indefinite strike for nearly a decade in Manipur, demanding the withdrawal of the APSPA from the state.
Several rights groups, including the powerful North East Students Organisation (NESO), have also demanded the withdrawal of AFSPA from the northeastern region.