Rajapaksa appeared before the Financial Crimes Investigations Division to record a statement and was arrested after he was questioned by the officers, Xinhua news agency reported.
He will be presented before a court later on Monday.
Rajapaksa was arrested on charges of misappropriating millions of rupees of the Divi Neguma funds which came under his ministry during the previous government.
This is the third time he has been arrested after his brother's defeat in a presidential election early last year.
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