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Mr Rajapaksa, 76, had sent his letter of resignation to his younger brother, President Gotabaya Rajapaksa, clearing the way for a "new unity government".
The biggest clashes since the economic crisis hit the island nation started this morning when supporters of the Rajapaksa family went on the rampage.
Protesters set fire to the official residences of Sri Lanka's Moratuwa Mayor Saman Lal Fernando and the MPs Sanath Nishantha, Ramesh Pathirana, and Nimal Lanza.
The police fired tear gas shells and water cannon and declared an immediate curfew in Colombo, which was later widened to span the country of 22 millon people. Dozens of buses used by Rajapaksa loyalists to travel to Colombo earlier in the day were torched or damaged across the country.
The island nation is experiencing acute shortages of food, fuel and other essentials, a crisis that has inflicted widespread misery and triggered weeks of mass demonstrations.