The ministry said: "According to the available information the bomb has been exploded at the Nugegoda Junction ... and a bus has caught fire after the attack."
Manik de Silva, editor of the Sunday Island newspaper, said: "There is no clear indication of how the blast was set off. The most likely possibility is that somebody left a package ... There was a lot of panic ... streets were crowded at that time so it created a lot of damage."
The earlier attack targeted Douglas Devananda, the social welfare minister, and was also believed to have been carried out by the separatist Tamil Tigers.
Devananda, the leader of the Eelam People's Democratic Party (EPDP), escaped unhurt.
Pushpa Soysa, spokeswoman for the Colombo national hospital, said two men from the minister's security staff were wounded in the blast.
"At 8:05am today an LTTE [Liberation Tigers of Tamil Eelam] handicapped female suicide cadre exploded herself at the office of minister Douglas Devananda," in the heart of the Sri Lanka capital, the defence ministry said in a statement.
Devananda is a vocal opponent of the LTTE, having once fought alongside the rebels before turning to politics in the 1980s.
The minister has survived at least four previous assassination attempts on his life, one of which was by a female suicide bomber in 2004.
'Waste of time'
Wednesday's attacks came a day after Velupillai Prabhakaran, the LTTE chief, declared Sri Lankan peace efforts a waste of time and vowed to strike back at the island's "genocidal" government.
"Those who plan to destroy the Tamil nation will in the end be forced to face their own destruction," he said.
A reclusive leader, Prabhakaran launched a furious assault on the island's Sinhalese majority, accusing "the Sinhala nation of trying to destroy the Tamil nation".
"It is unleashing unthinkable violence against another people. It only desires to find a solution to the Tamil question through military might and oppression," he said.
Gotabhaya Rajapakse, Sri Lanka's defence secretary, said on Monday, that his forces were aiming to kill Prabhakaran and recapture the northern part if the country.