"The oath-taking ceremony is an august occasion to celebrate democracy, not one that should be devalued by any political party which uses it as an opportunity to score political points," Banerjee said in a social media post.
The Trinamool Congress chief's reaction came after media reports said at least 70 family members of slain Bharatiya Janata Party (BJP) activists in West Bengal had been invited to the ceremony as "special guests".
This is being seen as a message to Banerjee ahead of Assembly elections scheduled in 2021.
The Chief Minister took exception to the BJP's claim that 54 people had been "murdered in political violence" in her state.
Congratulating Modi for taking over as the Prime Minister again, Banerjee said she did plan "to accept the constitutional invitation" and attend the oath-taking ceremony.
"However, in the past one hour, I am seeing media reports with the BJP claiming that 54 people have been murdered in political violence in Bengal," she said.
Calling the claim "completely untrue", she said: "There have been no political murders in Bengal."
Banerjee said the deaths may have occurred due to "personal enmity, family quarrels and other disputes, nothing related to politics".
"There is no such record with us," she added.
Earlier, BJP state Secretary Tushar Kanti Ghosh told : "The special guests including the kin of Sishupal Sahish, Trilochan Mahato and Dulal Kumar, who were killed and hanged from trees in Bengal's Purulia district will be taken to New Delhi by Rajdhani Express."
He said they were scheduled to return on Friday.
During the Lok Sabha election campaign, Modi and BJP President Amit Shah repeatedly highlighted the issue of violence directed at their party in West Bengal.
( With inputs from IANS )