The charge sheet filed before a court in Berhampore alleged that Chowdhury conspired in the murder of Trinamool Congress worker Kamal Sheikh in Golabazar area of the district in 2011.
Additional Chief Judicial Magistrate of district court, Ali Biswas, had yesterday issued the non-bailable arrest warrant against the minister.
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"I have been falsely implicated in this case. I will soon give a full report to Prime Minister Manmohan Singh and Congress President Sonia Gandhi," Chowdhury told PTI from Delhi.
"The Mamata Banerjee government has been trying to use police to stifle the voice of the Opposition," he said.
"They are following the same tactics pursued by the Left Front government to destroy democracy in the state," he said.
Chowdhury said he was not bothered by the case. "The police have been implicating Congress leaders in false cases to weaken the Congress in the state.
"I will inform the Prime Minister and Congress president about the autocratic rule in West Bengal," he said.
WBPCC President Pradip Bhattacharjee termed it as vindictive politics by the Trinamool Congress government.
Congress supporters blocked roads in Murshidabad and took out processions in all 26 blocks of the district in protest.
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