The LTTE said bombs fell near the offices of a charity that helps victims of landmines.
The rebels said the air force had bombed the same area on Tuesday and wounded four civilians who were admitted to the Puthukkudiyiruppu hospital.
Sri Lankan jets have been routinely bombing suspected rebel positions in the island's northeast since April last year.
The air force suffered a humiliating attack last week when Tiger aircraft bombed its main base next to the island's only international airport in Colombo and escaped unchallenged.
The Tamil rebels have waged a 35-year campaign for independence that has claimed more than 60,000 lives.
More than 4,000 people have been killed in the latest surge in fighting that began in December 2005, despite a truce arranged in 2002.