Heavy shelling was heard in Pampaimadu in the district of Vavuniya, which borders the rebel-held Wanni region, residents and officials said.
There were no details of the extent of the clashes, but military officials said reinforcements had been rushed to the area.
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Residents in Vavuniya, 256 kilometres (160 miles) north of here said they heard heavy shelling.
Earlier in the day, three rebels were shot dead by security forces in a separate confrontation along the de facto border separating rebel-held territory from the rest of the country, officials said.
The latest night-time clash in the north erupted hours after the air force bombed suspected Tamil Tiger positions in the island's east.
Fighter aircraft bombed the jungles of Thoppigala in the eastern district of Batticaloa on Saturday morning, the defence ministry said. It gave no further details.
Government troops and Tamil rebels have been locked in combat following the breakdown of a 2002 Norwegian-arranged truce. <