Led by party chief Vaiko, MDMK cadres Sunday staged a black flag demonstration against Prime Minister Narendra Modi shortly before he arrived here, accusing him of betraying the interests of Tamil Nadu.
Police said more than 100 protesters were detained and later let off.
Earlier, a scuffle broke out between the Police and the MDMK cadres as the police asked them to diperse.
Releasing black baloons, the protesting party cadres raised slogans against Modi alleging that he betrayed the interests of Tamil Nadu on Cauvery and other issues.
The Prime Minister arrived at the airport here about 30 minutes later and is scheduled to lay the foundation stone for the All India Institute of Medical Sciences near here and also address a public meeting.
The protest was held near the Periyar bus stand in the city, away from the venue of the AIIMS site and not in the route taken by the Prime Minister from the airport.
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In a counter move, BJP youth wing supporters put up posters sarcastically "welcoming Vaiko".
"We are here to welcome you and give a send off to you," the posters read.
The MDMK cadres claimed that the centre had accorded "permission to projects like neutrino and hydrocarbon extraction" which, according to them, would have an adverse impact on the livelihood of the farmers and also affect the common people.
On the Cauvery issue, they alleged that the Centre was supportive of Karnataka's bid to build a dam at Mekedatu across the river by giving permission for preparing a detailed project report.
The MDMK cadres, however, said the protest was not against the AIIMS.
Slogans like "go back Modi," and counter hashtags "Madurai thanks Modi," and "TN welcomes Modi" trended on micro blogging site Twitter.
Tamil Nadu unit BJP president Tamilisai Soundararajan and Union Minister of State for Finance and Shipping Pon Radhakrishnan strongly condemned MDMK for staging the protest ahead of the prime minister laying the foundation for a big project beneficial to the state.
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