The deaths mark some of the worst bloodshed in the region in years.
The troop deployment began as a general strike - called to protest against the killings - shut down the predominantly Hindu Jammu region of Indian Kashmir, where some half a million soldiers and policemen are deployed.
Suspected Islamist fighters shot dead 22 Hindus in two villages in the mountains of Doda district, 170 km (106 miles) northeast of Jammu, Kashmir's winter capital, early on Monday.
On the same day, the nine bullet-riddled bodies of Hindus were found in the neighbouring district of Udhampur. Four more bodies had been found in the same area on Sunday.
"We are definitely augmenting troop levels to prevent easier movement of militants in these areas," a senior police officer said.
An Islamist revolt against Indian rule in the disputed region - claimed both by India and Pakistan and ruled by them in parts - has killed more than 45,000 people since 1989.
The attacks came as India and Pakistan launched a fresh round of discussions to boost links between the two parts of Kashmir under their control, including the opening of up more crossing points and the movement of goods across the heavily-militarised frontier.
Separately, the Indian prime minister was due to begin talks on Wednesday with Kashmir's main political separatist alliance, the All Parties Hurriyat Conference, to find a way to resolve the decades-old conflict in the region.
"These are attempts to disrupt [the peace talks] but we are not going to be cowed down by that," India's national security adviser, MK Narayanan, told NDTV, an Indian news channel.
"We know how to deal with the situation."
Schools, banks and offices in Doda and Udhampur districts were closed following the strike call and traffic was largely limited to security vehicles and government cars.
Some Indian officials say the massacre could be a response to high voter turnout in by-elections last week in Doda, and could be aimed at souring the mood ahead of Wednesday's talks.
"We have seen so much bloodshed that some of have us have become insensitive"
Thakur Dass, resident
Residents of Kashmir, a region that triggered two of the three India-Pakistan wars, said they were weary of violence.
"We have seen so much bloodshed that some of have us have become insensitive. These killings should end," said Thakur Dass, who was visiting a relative wounded in the Doda attack.
Pakistan condemned the killings.
"The killing... in Doda district is unfortunate," Tasnim Aslam, a Pakistani foreign ministry spokeswoman, said.
"It is a terrorist act and we condemn it. [But] it will not have any impact on the peace process," she said.