"A particular national political party, along with one media house of Bengal, is constantly engaged in maligning state political personalities of the ruling party", Banerjee said without naming BJP and not referring to Sarada chit fund scam.
"It is very unfortunate that this vilification campaign is being repeatedly spread by different central agencies and without documents/proof," she said.
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"It is a sad time for democracy," Trinamool Congress supremo said in a Facebook post.
"The ruling party at the Centre should not bulldoze the regional parties and destabilize the federal structure", she said.
Recently, she had accused BJP of pursuing a "political vendetta" against TMC for political gains in the state, referring to the CBI probe in the Saradha scam.
Banerjee's comment came at a time when Trinamool Congress apparently finds itself in a corner in West Bengal over the ongoing probe in the Saradha ponzi scam in which some of its leaders have faced interrogation by CBI.
Transport Minister Madan Mitra and party MP Srinjoy Bose have been been arrested in connection with the scam. TMC general secretary Mukul Roy has been called by CBI to appear before it in connection with the scam.
Banerjee had recently charged that the investigating agency was being used as a "political tool" by the Centre and vowed to fight it "politically."
"CBI is being used for political vendetta. If you ask me the role of CBI, (it is) A-political vendetta, B-political-vendetta, C-political vendetta," she had said recently.