"Our troops were not involved in any firing. There may be some problem on their own side," Nadeem Raza, a spokesman for Pakistan's paramilitary Rangers, said.
Area commanders from the two sides were due to meet later on Wednesday to settle the matter, Raza said.
The foreign secretaries of the two countries will meet on Thursday for talks that could eventually pave the way for the resumption of the formal peace process broken off after the Mumbai assault that killed 166 people.
Deaths in Sopore
There has been a spate of clashes in the past few months along the Line of Control, the de facto border dividing mostly Muslim Kashmir between India and Pakistan.
In the latest such incident, three Indian soldiers and three alleged fighters were killed in a 24-hour gun battle in Sopore, 55km northwest of Srinagar, Kashmir's main city, police said.
The fighting began early on Tuesday.
The soldiers and two suspected fighters were killed later the same evening, an Indian army spokesman said.
Another suspected fighter was shot dead on Wednesday, he said.