"We are not afraid, we will continue to fight," Chryssohoidis told journalists at the ministry's entrance after the bombing.
The bomb, disguised as a gift, exploded on the seventh-floor office of the ministry's head of security, police said.
No one immediately claimed responsibility for the attack.
However, blame is being aimed at radical groups opposed to the government's economic and social policies.
"At a time when our country and our people are waging a daily battle to bring us out of the [financial] crisis, cowardly murderers want to undermine normality and our democracy..."
Greek prime minister
In recent years such groups have stepped up attacks although they have subsequently been faced with a police crackdown.
"I express my pain and exasperation - pain and exasperation that every Greek citizen feels over today's terrorist attack,'' George Papandreou, the prime minister, said.
"At a time when our country and our people are waging a daily battle to bring us out of the [financial] crisis, cowardly murderers want to undermine normality and our democracy ... and the sacrifices the Greek people are making to set the country on its feet,'' Papandreou said in a statement.
The bombing marks the first time in Greece that an attack has targeted the heart of the country's security apparatus, with a heavy police presence deployed at the ministry's entrance.
The building, on the outskirts of Athens, was evacuated after the explosion.
Greece is in the throws of financial crisis, with huge debts forcing the adoption of $110bn EU and International Monetary Fund rescue loans.
Subsequent government spending cuts have led to social unrest, with violent protests occuring in Athens.