Mohammed Kamel Mohammed Khalifa was sentenced to flogging after he said his son was sexually assaulted by a Saudi school headmaster.
The Egyptian Organisation for Human Rights had appealed to Saudi officials not to carry out the sentence, but the group's president, Nigad el-Borai, said that he was not surprised the Saudis ignored his plea.
"Saudi Arabia does not abide by international human rights conventions because it considers them against Islam," Mr el-Borai said. "The Saudis have no respectable judiciary. They still carry out these inhuman physical penalties like flogging." He added: "We are surprised at the Egyptian government's lack of interest, probably because political relations intervened."
Mr Khalifa was sentenced by a Saudi court to 200 lashes last September. His sentence was commuted to 80 lashes by an Appeals Court.