The latest fighting occurred near the abandoned border village of Shala Bhata, where the army says its troops have been battling dozens of armed rebels for 12 days.
There was no independent confirmation of the incidents.
Lt. Gen. Gurmeet Singh, an Indian army commander in Kashmir, said Wednesday that Indian soldiers encountered up to 40 rebels on Sept. 24 in Shala Bhata.
He said 12 militants were killed and five Indian soldiers wounded in the fighting at Shala Bhata, which is about 150 kilometers (95 miles) northwest of Srinagar, the main city in Indian-held Kashmir.
The commander denied Indian media reports that some Pakistani soldiers had occupied the village or any Indian military outposts there.
However, he suggested that some Pakistani special troops might be among the infiltrators.
The Pakistani military denied its troops had crossed the disputed border into Indian-controlled territory.
A senior Indian police officer, however, said some intruders had occupied some forward Indian posts in Shala Bhata. The officer spoke on condition of anonymity because of the sensitivity of the matter.
India and Pakistan have fought two wars over control of Kashmir since they gained independence from Britain in 1947, while rebel groups have been fighting since 1989 for independence or for merger with neighboring Pakistan, though most resistance is now shown through street protests.
An estimated 68,000 people have been killed in the conflict.
A 2003 cease-fire agreement between India and Pakistan has largely calmed the disputed Kashmir border. But the two sides occasionally accuse each other of violating it by firing mortars or gunshots.
India has long accused Pakistan of training and arming Kashmiri militants. Pakistan denies this and says it only gives moral and diplomatic support.