NEW DELHI — Indian security forces killed two militants, including a top commander, in a gun battle in the Kashmir Valley on Tuesday morning that also left one civilian dead.

The two militants belonged to Lashkar-e-Taiba, the Pakistani-based group that has long operated in the valley.

The commander, known as Abu Dujana, and the second militant were hiding out in a house in a village in Pulwama district when the Indian security forces ambushed it, officials said at a news conference in Srinagar, the summer capital of Jammu and Kashmir State.

Civilians rushed to the scene to protest the presence of the security forces, a frequent response to operations against militants in recent years. Separatist sentiment runs high in the valley, and a high level of militarization has led to disaffection with the Indian state and its tactics against civilians.