Pheko claimed she received her PhD from the American La Salle University in 2000.
However, the university closed in 1996 when it emerged it was selling degrees and other academic qualifications via the internet, the broadcaster reported.
Pheko told the SABC the university was promoted as legitimate and that she had registered at it, but it closed before she could be awarded her doctorate.
She told the broadcaster she still addressed herself as doctor.
Pheko joins the list of South African public officials who have fraudulently claimed to have certain academic qualifications. They include senior member of the ANC and former MP Pallo Jordan, and former SABC chairwoman Ellen Tshabalala.
The Democratic Alliance on Friday called for Pheko to be suspended.
“The DA calls for the immediate recalling and suspension of South African Ambassador to Japan, Ms Mohau Pheko, pending an inquiry for misrepresenting her qualifications,” MP Sandy Kalyan said.
The party claimed President Jacob Zuma was made aware of Pheko’s fraudulent degree in 2010, when she was appointed ambassador to Canada.
“Nothing less than a full parliamentary inquiry into this international blunder is needed to consider not only Ms Pheko’s conduct, but that of the presidency and dirco [department of international relations and co-operation] as well, given that government has turned a blind eye to this issue for several years.”