The Aug 30 order gives the areas rights akin to those of Pakistan's four provinces, but without actually conferring such a status constitutionally.
The region, now renamed Gilgit-Baltistan, will vote for a legislative assembly and will be governed by a chief minister, replacing direct rule by Islamabad.
The Northern Areas are seen by both India and Pakistan as part of the larger Jammu and Kashmir issue which they are trying to resolve in their composite dialogue.
New Delhi also protested the 7,000 MW Bunji hydroelectric project being built in the Pakistan-administered Kashmir with Chinese assistance.
'The government of India lodged a protest today over the proposed construction of the Bunji hydroelectric project in a part of the state of Jammu and Kashmir under illegal occupation of Pakistan,' external affairs ministry spokesperson Vishnu Prakash told reporters while reading from a statement.
Pakistan and China signed a memorandum of understanding in August for the construction of a dam at Bunji in Astore district in Gilgit-Baltistan, earlier known as the Northern Areas, during President Asif Ali Zardari's Beijing visit.
Earlier, New Delhi had also protested the construction of the Neelam Jhelum hydropower project and Bhasa dam in what it calls Pakistan-Occupied Kashmir, which is referred to as 'Azaad Kashmir' by Islamabad.
The dam, one of the eight hydel projects shortlisted for construction with a capacity of generating 7,000 MW of electricity, has triggered anxieties in India about growing Chinese activities in Pakistani Kashmir.