Senior minister Jeyaraj Fernandopulle, 55, was killed in the town of Weliveriya outside of the capital when the blast ripped through the large gathering at the event, police said.
The minister had walked up to the starting line where more than 100 athletes had lined up and at the count down a huge blast shattered the occasion.
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"Ready, on your marks, steady...," the official had said over the public address system, moments before the huge explosion.
"It was a suicide bombing of the Tigers," media minister Anura Yapa said.
Fernandopulle, a vocal critic of the separatist Tamil Tiger rebels and a member of Sri Lanka's failed peace talks with the guerrillas, is the second government minister to be killed this year.
Television footage showed an explosion close to the minister, the Leader of the House in parliament and regarded as a potential prime minister, at the start of the marathon.
"We suspect a suicide bomber pretending to be a marathon runner carried out the attack,