The Maoist insurgency - waged mostly from the vast, mineral-rich forests of central and eastern India by rebels who say they are fighting for the rights of the poor and landless - has grown bloodier in recent months, with hundreds dying in attacks.
But as poorly trained security forces struggle to quell the growing rebellion, New Delhi has found another group to do battle with.
"The government seems to think that civil society organisations, rights activists and intellectuals have more than just an academic interest in the issue and may be serving as front organisations for the Maoists," said Meenakshi Ganguly of Human Rights Watch.
"But the problem is they have not really named these organisations and so every civil society group in India is at risk of being targeted by local authorities for being pro-Maoist."
India, the world's largest democracy, has a strong civil society that has rarely shied away from criticising government policy and violations by security forces in conflict areas like Kashmir and the northeast.
WAR OF WORDS
Human rights campaigners, writers, judges and aid workers have spoken out against tactics in India's mineral belt, where the authorities are accused of trying to force poor tribes people from their forest villages to make way for mining corporations.
They have also called for investigations into alleged abuses by government-backed vigilantes, including arbitrary arrests, torture and killings of tribal villagers.
But condemnation of the actions of paramilitary forces and policemen by high-profile writers and activists like Booker-prize winner Arundhati Roy has prompted some to brand them as anti-nationalist and Maoist sympathisers.
And following a spate of major rebel attacks over the last two months, India's interior minister - under pressure to deal with what Prime Minister Manmohan Singh has called "India's biggest internal security threat" - has laid the blame at the door of civil society groups.
"I agree, the government has to answer a lot too, the government has certain questions pertaining to human rights violations. Likewise, shouldn't civil society organisations answer for what happened today?" Palaniappan Chidambaram told local news station NDTV, after more than 30 people died when their bus was blown up on May 17.
The rebels are accused of recruiting people by force, including children, and widespread extortion. They have attacked schools and police stations, and use landmines and improvised explosive devices in areas where civilians live.
They have also hijacked passenger trains, and beheaded policemen and villagers suspected of being police informers.
Chidambaram has blamed activists for having a partial perspective, accusing them of criticising the government but sparing the Maoists, and thereby legitimising their violent tactics.
"They (civil society) question the legitimacy of state power, they question the objectives that government has set for itself in these anti-Maoist operations...but they won't condemn the wanton, deliberate, cruel, heartless violence that has happened?"
"And if the civil society organisations rush to condemn government, but won't say a word on the bus attack...then that's a bloody sad commentary on the state of our civil society organisations," he added.
FRONT ORGANISATIONS?
The government's displeasure with civil society groups runs much deeper than concerns over biased comments.
Indian investigative magazine Tehelka recently quoted an Intelligence Bureau communique which claimed that the Maoists had "57 front bodies working among the peasants, labourers, women, students, tribals, backward classes etc."
It said these groups "supplement the activities of the armed cadres and mobilise the masses ostensibly for the cause of the people, but primarily for the cause of the party".
It claimed such groups are working with poor, marginalised communities to influence them with leftist ideologies and recruit them to take up arms against the state.
Groups like the People's Union for Civil Liberties - India's largest and oldest human rights group - as well as the Association for the Protection of Democratic Rights and the Peoples Union for Democratic Rights were mentioned in the communique, according to the report.
Non-profit groups and activists are angry at being labelled front organisations for the Maoists.
"We work for the people and while we may agree with the rebels on issues such as the lack of rights of tribes people and their forceful displacement, that does not mean that we support their violence and tactics," said one activist.
Others said it is difficult to speak out against the Maoists in public because doing so would jeopardise their development work on projects in villages under rebel control.
CRACKDOWN FEARS
Independent observers in the region say local journalists, aid workers and other NGO employees have been subjected for years to harassment by the state including arbitrary arrests, detentions and having their movement curtailed.
They cite cases like that of doctor and human rights activist Binayak Sen, who was providing medical assistance to tribal villagers when he was arrested and jailed for two years, accused of having links with the Maoists.
Himanshu Kumar, a Gandhian and activist who worked in Chhattisgarh's troubled Dantewada district, said he was one of many persecuted for speaking out against violations committed by the police and state-backed militias.
"They demolished the ashram and accused me of kidnapping a witness who had actually come to me for protection," said the director of Vanvasi Chetna Ashram, a development NGO. "They want to stamp out any dissent."
Observers say some groups may support the Maoists, but rights-based organisations, NGOs working on poverty alleviation, intellectuals and academics are increasingly being tarred with the same brush, leaving many at risk of repression.
"There may be pro-Maoists groups out there but the government has to publicly name and shame them, produce the necessary evidence and crack down on them," said one employee of an international humanitarian agency in the region.
"The accusations of the government in Delhi are basically a green light to local authorities and security forces to do whatever they want...even to those who are genuinely trying to improve the lives of some of the poorest in India."