Jan Jambon is the right-hand man of Bart De Wever, whose nationalist New Flemish Alliance (N-VA), based in Belgium's north, dominates the centre-right coalition led by Prime Minister Charles Michel from the French-speaking south.
"The people who collaborated with the Germans had their reasons," Jambon told La Libre Belgique daily, noting that he was not alive at the time to judge.
The new coalition was sworn in on Saturday and faces a vote of confidence in parliament Thursday which it is expected to win.
"I defy anyone to find a phrase, a text where I defend collaboration. Collaboration was a mistake," Jambon told La Libre Belgique.
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He said he had already explained his presence at the meeting where he spoke for the VVB Flemish populist movement, of which he remains a member.
In a statement later today, Jambon forcefully rejected any suggestion he condoned collaboration and said his comments had been taken out of context and maliciously exploited.
"If my words were misunderstood and caused offence, I regret it," he added.
Belgium's wartime history is a divisive chapter in an already sharply divided country, where the split between the Flemish and French-speaking communities led to a five-month delay in forming the new government.