"Selective raids and arrest have been made against one faction of the AIADMK," he said.
Income Tax raids were carried out against Tamil Nadu Health Minister C Vijayabaskar while leader of the AIADMK (Amma) faction, T T V Dhinakaran has arrested by Delhi police in a case of alleged bribing of an Election Commission official to secure the party's coveted 'two leaves' symbol.
He alleged that the BJP government was behind the raids and related developments.
"The Prime Minister should stop use of agencies like IT, ED and CBI by BJP for politics," he said.
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He also urged Modi to ensure that the state government is run as per the Constitution.
In a video put up on his Twitter page,Stalin also slammed the Centre on issues concerning Tamil Nadu, saying it was not showing any inclination to address it's problems like the fishermens' issue and inter-state water disputes.
People were struggling to meet their drinking water needs on account of severe drought, but the Centre had not offered any assistance, he charged.
The state government administration has also come to a 'standstill' ever since late chief Minister J Jayalalithaa was admitted to hospital in September 2016, he said.