Gen Prayuth Chan-ocha, chief of the National Council for Peace and Order (NCPO), issued the order on Friday.
Farmers in the provinces have had problems transporting their produce amid violence in the region and the supply has accumulated to 6,100 tonnes for mangosteen and 10,400 tonnes for longgong.
The Ministry of Commerce was also assigned to help market the fruit nationwide.
In the meantime, the NCPO plans to spend 6.7 billion baht from the government's central fund to help farmers. About 1 billion baht was disbursed and the council wants to spend the whole sum within this month.