As the soldiers were carrying out their search the bomb exploded, Samarasinghe said.
Ampara was the scene of bitter fighting last month between government forces and the rebels as the army fought to oust the rebels from bases they hold in the east.
There was no immediate claim of responsibility for the bombing.
The Liberation Tigers of Tamil Eelam rebels have fought the government since 1983 to create an independent homeland after decades of discrimination by the Sinhalese-dominated state.
The Tamil represent a 3.1 million minority in the north and east of the island. At least 69,000 people have died in the violence.