Mentioning the gun battle that erupted Thursday in Jammu and Kashmir's Arnia sector, he said Pakistan's claim that "non state actors are behind such incidents is not true".
He was addressing the 49th All India DGPs and IGPs conference here.
Eleven people - four civilians, three soldiers and four militants - were killed in the fierce gunfight that ended Friday.
Rajnath Singh also raised the Islamic State (IS) issue at the conference and described the terror group as a "major security threat". "We are concerned about the fact that Indian youngsters are getting drawn to Islamic State."
The home minister said Al-Qaida is a serious threat and the central government has not taken it lightly.
"There may be many terrorist organisations in the world but the government will not allow them to get a foothold in India," he said.
He said "Muslims fought for India's freedom like Hindus did. Al-Qaida won't succeed in their motives."
On the Oct 2 Burdwan blast, he said the West Bengal Police and National Investigation Agency are playing crucial roles in the probe.
The blast took place at a house in Burdwan district's Khagragarh area, killing two Jamaat-ul-Mujahideen Bangladesh militants and injuring another.
Admitting that there was lack of development in the northeast, he said: "There is lack of development in northeast. Let me assure you, we are committed towards a comprehensive development of this region."
Singh urged all the northeastern states to fill up vacancies in the police forces and assured them of all possible help.
Directors general of police (DGPs), inspectors general of police (IGPs) from all states and union territories, heads of all paramilitary forces, officials from the Intelligence Bureau and all chief ministers of the northeastern states are taking part in the two-day conference.