According to a Union Home Ministry notification, the decision was taken after considering the present law and order situation in the six districts of the state.
As per the notification, the three districts of Arunachal Pradesh, which will continue to be designated as disturbed areas under AFSPA are Tirap, Changlang and Longding.
The designation, which allows imposition of AFSPA, will also continue for the four police stations areas of the state's three other districts bordering Assam.
They include Namsai and Mahadevpur police stations in Namsai district, Roing in Lower Dibang Valley district and Sunpura in Lohit district.
A home ministry official said the "disturbed area" tag was withdrawn from the four police station areas of the Arunchal's districts on Assam border, due to the improvement of law and order situation there.
The notification said the Union Home Ministry took the decision exercising its powers conferred under section 3 of the Armed Forces (Special Powers) Act, 1958.
A review of the law and order situation in Arunachal's six districts was undertaken before the March 31 deadline for the validity of the "disturbed area" designation under the AFSPA.
The AFSPA is imposed in areas where armed forces are required to operate in aid to civil authorities. For AFSPA to become valid, an area, however, needs to be declared disturbed either by the Central or the state government under the section 3 of the 1958 Act.
Some parts of Arunachal Pradesh has presence of banned militant outfits like NSCN, ULFA and NDFB, another official said.