There has been a sudden spike in the applications at the commissioner's office, mostly from Muslims who say they fear for their lives after unrest of 2016 following the death of Hizbul Mujahideen terrorist Burhan Wani.
"The political workers who were on the target of militants in the '90s and left the Valley are still not safe. The militants are still after them," said Ghulam Rasool Wani.
The registration of migrants was stopped in 2008, and the decision to allow fresh applications was taken last year, but now the commissioner's office has started accepting applications.
The migrant status will entitle them to the same benefits as Kashmiri pandit migrants. Each pandit family receives cash assistance of Rs 10,000 besides free accommodation, ration and reservation in some professional colleges.
The issue has snowballed into a major political controversy. The BJP says the migration of Muslims can change the demographics of Jammu district, but the PDP disagrees.
"We have put forth our views before the government, it is not acceptable from Jammu's point of view and no migration from Kashmir to Jammu can take place," said Arun Gupta, BJP's state spokesperson.
"They have to go through a process," said senior PDP leader Nizam ud din Bhat.
There are nearly 60,000 Kashmiri families registered as migrants across the country and of them about 38,000 families live in Jammu.
Fresh registration of migrants could trigger a new political controversy in the state but essentially this runs against the spirit of resolution passed by the state assembly to create conducive atmosphere for the return of Kashmiri pandits.