He said the Naxals were spreading in urban areas and were trying to mislead the people.
Fadnavis told reporters that the two letters, allegedly from Maoist organisations, threatened him and his family and were handed over to the police.
The letters were received by the chief minister's office a week ago, sources in the state Home Department said today.
"The letters came after the recent anti-Naxal operations in Gadchiroli, in which 39 Maoists were killed. The letters have been handed over to the police for further investigations," the sources said.
Both letters mentioned the Gadchiroli encounters.
The chief minister said police have recovered evidence that the Maoists were hatching a conspiracy to target Prime Minister Narendra Modi, Pune police, who have arrested five persons for alleged Maoist links, yesterday claimed that the ultras were planning to target the prime minister.
"Earlier Naxals were confined to rural areas, now they have spread to urban areas," Fadnavis .
"They are on a mission and trying to mislead people," he said.
"In one of the internal communications (recovered from houses of those arrested by Pune police) a commander has directed his cadre that Modi should be eliminated the way Rajiv Gandhi was assassinated.
"Many such communications have been seized during the raids. The intelligence agencies are at work and investigators are probing more links," said Fadnavis, who also handles the home portfolio.
A letter found in the house of a person arrested for alleged Maoist "links" talks about the ultras mulling "Rajiv Gandhi-type incident" and suggesting that Prime Minister Narendra Modi should be targeted during his road shows, according to the police.
The letter, addressed to one Comrade Prakash by sender who identifies himself as 'R', talks about the requirement of Rs 8 crore to procure M-4 rifle along with four lakh rounds of ammunition for the purpose.
The letter was allegedly recovered from the house of Rona Wilson who was among five people arrested from Mumbai, Nagpur and Delhi in connection with 'Elgar Parishad' held in Pune in December and the subsequent Bhima-Koregaon violence in the district, the police said.
All the five were yesterday produced before the sessions court in Pune which remanded them in police custody till June 14.
Rajiv Gandhi, former prime minister, was killed by a woman suicide bomber during a public event in Sriperumbudur in Tamil Nadu on May 21, 1991.