Jaliya Wickremasuriya was arrested by police's Financial Crimes Investigation Division (FCID) last night from the Colombo international airport for alleged misappropriation of 3 million rupees.
He was remandedin to police custody till December 2.
Wickremasuriya is a cousin of Rajapaksa. His arrest comes as many of Rajapaksa's family members have faced prosecution since the strongman was defeated by Maithripala Sirisena in the presidential election last year.
Rajapaksas have slammed the action against them as a political witch hunt.