Tifatul Sembiring said he doesn't believe in shaking hands with women outside of his family.
But video of Sembiring meeting Michelle Obama, Sembiring seemed to be eagerly reaching out to make contact with the first lady.
While Indonesia has the largest Muslim population in the world, the vast majority practice a moderate form of the faith. But Sembiring has flaunted his conservatism.
His denial was in a response to tweets from Indonesians who noted the handshake and questioned his long-standing claims that, as a good Muslim, he restricts his contact with women.
Many posts had a "gotchya" quality to them.
Sembiring has often tweeted controversial comments, including blaming natural disasters on a lack of morality and joking about AIDS.
The Associated Press contributed to this story.