The ministry said its latest figures showed 5,036 rebels and 446 of its own soldiers had died in fighting between the start of the year and Friday night.
The Liberation Tigers of Tamil Eelam (LTTE), who have waged a bloody fight since 1972 for an independent homeland for ethnic Tamils, have not released their estimate of casualties.
Figures from both sides cannot be independently verified as journalists are barred from reporting from front line areas.
Meanwhile, at least 16 rebels and one soldier were killed in fighting across the north on Saturday, the ministry said.
The rebels did not comment on the fighting.
Sri Lankan troops have being trying since July last year to dismantle the de-facto separate state the rebels maintain in the north of the country, with fighting centred around Mannar, Jaffna, Weli Oya and Vavuniya.
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Army chief Lieutenant General Sarath Fonseka Saturday said forces had wiped out two-thirds of the LTTE's military capability and put its current streng