As more than 5,000 soldiers and police patrolled the restive tea-growing region, Home Minister Sushilkumar Shinde said the killings appeared aimed at provoking a "full fledged" communal conflict.
Police blame indigenous Bodo tribesmen for the violence on Thursday and Friday nights in the region, where Muslims have long been accused of grabbing land after migrating from across the Bangladesh border.
"The objective of this (separatist) group seems to be aimed at starting a full fledged communal conflagration," Shinde said in a statement, adding the violence was targeted at women and children.
"The public leaders of both Bodo and (the) minority community must see to it that things do not deteriorate," the minister said, urging the region to maintain "peace and calm".
The violence comes during the final stretch of the country's mammoth general election, which has seen religious and ethnic tensions flare and deadly attacks staged elsewhere in the country including by Maoist rebels.
Hindu nationalist hardliner Narendra Modi and his opposition Bharatiya Janata Party (BJP) are expected to defeat the ruling Congress party after a decade in power.
Thousands of families have fled their homes since masked gunmen went on the rampage in Baksa and neighbouring Kokrajhar district, shooting Muslims dead including children as young as 18 months as they slept.
Shinde put the death toll at 32. But a senior police official said two more bodies were discovered on Sunday while a teenager died of her injuries overnight Saturday, taking the number killed to 35.
"Two dead bodies were recovered from a riverbank a few kilometres away from Narayanguri while another teenage girl injured in the attack succumbed to her injuries in a hospital," the officer told AFP on condition of anonymity.
Some 4,000 Central Armed Police Force officers and 1,500 soldiers have already been deployed, with another 1,000 police on their way, Shinde's statement said.
Despite the tight security, Muslim community leader Ibrahim Ali told AFP families have fled their homes, some of which have been razed, adding that "a sense of fear and panic looms large".
"More than 5,000 people have fled their homes in the two districts and are taking shelter in safe areas," said Abdur Rahim, leader of the All Minority Students Union.
The victims are Muslims whose migrant community has long been locked in land disputes with Bodos that have spilled over into violence in the remote state that borders Bhutan and Bangladesh.
Local media reported that Bodos targeted the community as punishment for failing to support their candidate in the multi-phase election. Voting in Assam ended on April 24.
Modi, frontrunner for prime minister, said last week illegal immigrants from Bangladesh should pack their bags if he came to power at the polls, whose results are to be announced on May 16.
A political row has flared over the attacks, with Congress accusing the BJP of creating a "communal atmosphere" during the election.
The BJP in turn accused Congress, in power at state level in Assam, of failing to maintain law and order.
Muslims in Baksa refused on Sunday to bury 18 of those killed, in a protest against authorities whom they accuse of failing to protect them.
Police blame the National Democratic Front of Bodoland, one of several banned rebel groups demanding a separate homeland, for the attacks. The front has denied being behind the violence.
Seventeen people were killed in clashes in the same region in January and thousands of others fled their homes.
In 2012 ethnic clashes in the same area claimed about 100 lives and displaced more than 400,000 people.
COMMENTS (24)
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A dreadful sign of the things we can expect if the forces of communalism are strengthened by a BJP-RSS victory. Immediately after the massacres Modi is still talking about 'infiltrators', code for Bengali Muslims. Increased communal polarisation in the North East is the only way that the BJP can get a foothold in this region where they are historically weak.
Indian implosion has begun and will progress further after it establishes it as Hindutwa Bharat!! The Government of Pakistan and Bangla Desh must be prepared to expect a large movement of Indian muslims seeking refuge in their territories.
Rex Minor
@nkn: fyi 2000 people were killed in sectarian violence, not just shias. These 2000 include people from all sects.
When Hindus massacre Muslims, they become national heroes like Modi. It sets a bad precedent for future Hindu fanatics, giving them a green light to kill Muslims. The end result will be a future partition of India on religious lines. It seems inevitable now.
@Raj Kafir: "Pakistanis will still blame Narendra Modi whereas Congress is in power in the state of Assam" And, at the Centre!
@Last Word: The Bodo's are now 30% . of the population in their homeland?How does that feel say if it was Sind or Punjab
@Raj Kafir: Who is pak to blame!
We will protect all Indian citizens irrespective of their religion. The perpetrators of this crime will be found and severely punished. No excuses.
@Bakhtiyar Ghazi Khan: Genocide against Indian Muslims
Ignorant or just plain lying ? What was the percentage of minorities in India after partition and what is the percentage today ?
Now do the same exercise for Pakistan.
so two nation theory is wrong eh!
why muslims are in India when they got their homeland Pakistan and BD
This is the end result of Hindu extremism. Genocide against Indian Muslims, Christians, Sikhs, and Buddhists. If Modi gets elected, then the world will see the true face of Hindu fanatics.
@Tani:
The problem is not that of a separate Bodo state. The issue is that illegal Bangladesh migrants have been settling down in adjacent Indian states and often occupying lands that doesn't belong to them.
It is natural for the local population to be angered by such large-scale illegal immigration. For example, even today, native Sindhis are resentful of the Muhajirs who settled down in Sindh.
As a result of government inaction in protecting the border, the illegal BD population in India has now grown to over 20 millions.
Condemn the killings but such situations are hard to resist when traitors like Congress government of Assam allow illegal migrations for vote bank benefits. They have been anyways given a full landmass in the name of a country separate from Hindu India , then why are they coming back to us ?
Secularism at its peak
Prelude to the premiership of modi the mass murderer
Some mindless killing has been carried out by Bodo tribals who have a poor track record of attacking non-Bodos irrespective of one's religion. The influx of large number of Bangladeshi migrants in this region rattled Bodos as they feel threatened to become a minority besides their economy passing on to the foreigners. Handing over this region to the army is a good move who will bring the situation under control in a short time.
Pakistanis will still blame Narendra Modi whereas Congress is in power in the state of Assam
And there we have a "vibrant India" bent on exterminating peaceful Muslims from Indian occupied Kashmir to Assam. May Allah have mercy on poor souls there. Ameen.
Get rid of that hate monger Modi!
Reminder : in Pakistan last 6 years around 2000 shia's alone killed in sectarian killling
muslim nationalist pmln support laskher e jhangvi group - imran khan claim
2000 people alone killed every year in karachi - have anybody fix responsibility for navaz sharif, zardari
Imran khan is also called taliban khan
many muslims killed in china - why no news on that in pakistan ?
Why can't indian government give them separate state for bodo tribal animist and Christian practising religion people? It's been their long standing demand since decades for bodoland state. Is all this banned bodo militant group striking violence worth it? And what's with Assam govt giving shelter to Bangladeshi illegal refugees and immigrants in bodoland areas? Vote bank politics has a limit don't create Israel Palestine like situation its land of bodos. If the govt can't vacant illegal Bangladeshi migrants at least give bodos separate state end this terrorist attacks.
and there goes your democracy.........