The 29-year-old, who won gold in the women's 400m hurdles at the Athens Olympics, failed the test while in Japan this month preparing for the Beijing Games.
Her case first surfaced on Sunday when the Greek Olympic Committee suspended Halkia and ordered her out of the Olympic Village.
The IOC, in statement, said she tested positive for Methyltrienolone, a steroid with potentially serious side effects.
The test was conducted on August 10 with the IOC informed of the positive A sample last Saturday and the B sample on Sunday.
The IOC added that a feature of the case was that they had notified Greek authorities of their concerns regarding possible violations of Greek law by Chalkia's coach George Panagiotopoulos.
Her case takes the number of positive doping tests confirmed in Beijing to four after those of Spanish cyclist Maria Isobel Moreno, medal-winning North Korean shooter Kim Jong-Su and Vietnamese gymnast Do Thi Ngan Thuong.
Bulgarian 1500 metre runner Daniela Yordan