Mahinda Rajapakse told the state-run Daily News newspaper that his security forces were "fighting under severe constraints, to cause no harm or loss to innocent, civilian human life.
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"The battle against terrorism, which we could convincingly win within a few days, is nevertheless prolonged due to the grave concern and the optimum caution exercised by the highly disciplined armed forces," he said.
The president's remarks came a day after the defence ministry admitted that scores of its troops had been killed or injured in fighting with the rebel Liberation Tigers of Tamil Eelam (LTTE) over the weekend.
The defence ministry said troops had edged closer to the rebels' northern capital of Kilinochchi, but battles since Saturday had left 33 soldiers dead, three missing in action and 48 injured.
Rajapakse accused the LTTE of using "human shields.
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"We have directed the armed forces to refrain from inflicting any harm, even a scratch, to the innocent civilians who are being uti