The order released earlier this week would grant Pakistani federal government more authority on the ground than the local council.
"The Deputy High Commissioner of Pakistan to India was summoned today and a strong protest was made against Government of Pakistan’s so-called 'Gilgit Baltistan Order 2018'. It was clearly conveyed that the entire state of Jammu and Kashmir which also includes the so-called 'Gilgit-Baltistan' areas is an integral part of India by virtue of its accession in 1947," the statement read.
The ministry stressed that any changes to the status of the territory were illegal and unacceptable.
The UN Security Council's Resolution of 1947 places Gilgit-Baltistan within the Jammu and Kashmir region, claimed by both India and Pakistan. The area, split between India, Pakistan, and, to a smaller extent, China, has seen numerous conflicts and civilian unrest.