Gunmen killed Harry Abeyweera, the top civil administrator in the district of Trincomalee, as he worked at his office, police said.
Gunmen escaped and an investigation was under way.
The assassination came hours after the government announced it will mark the wresting of the Eastern Province from the Liberation Tigers of Tamil Eelam (LTTE) after dismantling a rebel base in the district of Batticaloa.
President Mahinda Rajapakse condemned the killing and said it was a blow to restore democracy.
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"This comes at a time when we are trying to restore democracy in the Eastern Province," a spokesman for the president said. Security forces took control of the entire region last week after dismantling the final rebel jungle base known as the Thoppigala complex.