The MDMK headed by Vaiko Monday quit the BJP-led coalition to protest against the government's stand on Sri Lanka and Tamil Nadu's water row with Kerala and Karnataka.
A high-level committee of the Tamil Nadu-based party passed a resolution to this effect here. The MDMK was the first party in Tamil Nadu to ally with the BJP ahead of the Lok Sabha election in May.
Reacting to the development, BJP leader and central minister Pon Radhakrishnan said this was not an happy development and the issues could have been sorted out by talks.
Radhakrishnan said alliances are formed in the firm belief that the parties will be together for five years.
Allies, he said, have a right to discuss with appropriate persons if they want a policy change.
The MDMK said that when it joined the National Democratic Alliance (NDA), it made it clear that the BJP-led government should not back Sri Lanka and its President Mahinda Rajapaksa.
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But Prime Minister Narendra Modi's government had gone against the earlier promises and started supporting the Rajapaksa government, it said.
The MDMK accuses the Rajapaksa regime of killing thousands of innocent Tamils during the final stages of the war that vanquished the Tamil Tigers in 2009.
The MDMK, which has no member in parliament, also found fault with the central government's language policy, saying it was trying to impose Hindi and pursuing "Sanskritisation".
Similarly, the party said the central government was betraying the interests of Tamil Nadu over the Mullaperiyar dam row with Kerala and on the sharing of Cauvery river water with Karnataka.
Vaiko's party complained that the central government had also failed to help the fishing community in Tamil Nadu vis-a-vis attacks and arrests by the Sri Lankan Navy.
Although the exit will in no way affect the central government, the MDMK becomes the first party to quit the BJP-led alliance since Modi took power in May this year.
A long-standing supporter of the Tamil Tigers, Vaiko has been critical of Modi for warming up to President Rajapaksa.
On Nov 26, the MDMK took a leading part in celebrating the 60th birth anniversary of the slain Tamil Tigers leader, Velupillai Prabhakaran, all over Tamil Nadu.