Soon after, radar picked up an unidentified aircraft heading south over the Indian Ocean towards Colombo.
The city was plunged into darkness after power was switched off as a precaution, jets were scrambled and anti-aircraft guns thundered from Colombo's shoreline.
But a Tigers aircraft still managed to drop bombs at Kelanitissa power station.
Nanayakkara said it was not clear whether the raids were carried out by the same aircraft.
Minelle Fernandez, reporting for Al Jazeera from Colombo, said the raids were a strong signal that the Tigers were still able to strike at the heart of the capital despite the military saying it had the separatists cornered.
The Tigers are locked in heavy fighting with the military in northern Sri Lanka, where the government has expressed confidence that it will defeat a foe its has battled since 1983 in one of Asia's longest-running separatist rebellion.
The military has stepped up its offensive in the last three months and says it has steadily seized one LTTE stronghold after another and is within striking distance of the rebel capital Kilinochchi.
Tens of thousands of people have died since the LTTE launched a separatist campaign in 1972 for a homeland for minority Tamils in the majority Sinhalese island's north and east.