The two --Alaa and Gamal - who have been in detention since April 2011, are on trial for insider trading. They were acquitted on June 2 of separate corruption charges.
They are being questioned in Tora prison by investigative judge Osama El-Seidy after former MP Essam Sultan accused Shafiq of selling state land to Mubarak's sons, al Ahram newspaper reported.
Sultan accused Shafiq last May of exploiting his position as head of Young Air Force Officers Association by selling thousands of acres of state land in Ismailiya, earmarked for the association, at reduced prices to Mubarak's sons.
Mubarak, who was ousted last year in a popular mass uprising, is now serving a life sentence for his role in the deaths of more than 800 protesters during the revolt.