"There is a presence of al-Qaeda militants in Kashmir," Vij told reporters during a visit to Kashmir's winter capital Jammu.
It is not the first time Indian officials have made the claim. Last year Defence Minister George Fernandes also said al-Qaeda was operating in Indian Kashmir.
Vij said 70 to 80 percent of militants in Kashmir were "coming from across the border and they are foreigners."
New Delhi accuses Pakistan of arming, funding and training Islamic rebels waging an anti-India rebellion in Kashmir since 1989. Pakistan denies the charge, saying it provides only moral and diplomatic support to an "indigenous" uprising in the Muslim-majority territory.
Vij ruled out the possibility of Indian and Pakistani troops jointly patrolling their disputed borders in Kashmir.
"How will joint patrolling help because Pakistan is sending in the militants?" he asked.
He said there were thousands of militants assembled on the Pakistani side waiting to infiltrate into Indian Kashmir.
There were 85 rebel training camps in Pakistani territory, many of which were merged with training centres for the Pakistani army, he said.
In September there were 28 attempts by Pakistan to push in rebels into India with Indian security forces killing 78 of the rebels, Vij said.
In October, Pakistan had made six such attempts and Indian troops had killed 65 rebels up until Saturday, he said.
The Himalyan region of Kashmir is divided between India and Pakistan and claimed in full by both.
The nuclear-armed rivals have fought two of their three wars over Kashmir and came to the brink of another conflict last year over Indian demands that Pakistan stop its support for rebels crossing the de facto border.
More than 39,500 people have died in Indian Kashmir since the eruption of the insurgency, according to official figures. Separatists put the toll at between 80,000 and 100,000.