Ms Sundar, 48, has been named in a complaint by the wife of Shamnath Baghel, who was killed by Maoists last Friday at his village in Bastar. "It is absurd, bizarre and patently malafide. I haven't been in Bastar in months, since May," she said.
The activists have been accused of murder, conspiracy and rioting, said senior police officer SRP Kalluri, adding that "strongest possible action" will be taken against those guilty.
"Activists are enemies because they incite the people of India," Mr Kalluri told NDTV.
Baghel was killed by Maoists on Friday at his village around 450 km from state capital Raipur. He had been leading a campaign against Maoist activities since April and had recently formed the "Tangiya (axe) group".
"The victim's wife has alleged that Nandini and other workers held meetings in the area and that was provocative. There were threats received that Baghel will be eliminated if he doesn't mend his ways," Mr Kalluri said.
"Nandini Sundar, to us, is a suspect; her behaviour from the start has been suspicious," he added.
Baghel and other villagers had reportedly complained in May against Ms Sundar.
The activist has accused the police officer of forcing Baghel's wife to file a complaint against her.
"This is clear vendetta. Mr Kalluri has been specifically targeting activists," she told NDTV, alleging that Mr Kalluri is worried about being implicated in a case that the activists have been fighting in court for years.
"I don't even remember (Baghel's) name. We told the villagers that they have to be independent, because they face danger from both sides," said Ms Sundar.
Ms Sundar heads the sociology department at the Delhi University. Her petition led to a landmark Supreme Court ruling that banned state-backed anti-Maoist militia Salwa Judum.