Hamza Kashgari, a 23-year-old columnist, sparked outrage in the oil-rich kingdom with comments posted on the Prophet's birthday a week ago that led some Islamic clerics to call for him to face the death penalty.
Kashgari fled the country, but was arrested by police in majority-Muslim Malaysia on Thursday as he transited through Kuala Lumpur international airport.
"The Saudi writer was repatriated to his home country this Sunday morning," a police spokesman told Reuters. "This is an internal Saudi matter that we cannot comment on."
Malaysia has a close affinity with many Middle Eastern nations through their shared religion. The Southeast Asian nation is also a U.S. ally and a leading global voice for moderate Islam, meaning that the decision to extradite Kashgari is certain to be controversial.
"Saudi clerics have already made up their mind that Kashgari is an apostate who must face punishment," Christoph Wilcke, senior Middle East researcher at Human Rights Watch, said in a statement on Friday.
"The Malaysian government should not be complicit in sealing Kashgari's fate by sending him back."
Kashgari's lawyer in Malaysia, Mohammad Noor, told Reuters by telephone that he had obtained a court order to prevent the deportation, but had not been allowed to see his client. "If the government of Malaysia deports him to Saudi Arabia, disrespecting the court order, this is clearly contempt of court, unlawful and unacceptable," he said.
The Star newspaper quoted Home Minister Hishammuddin Hussein as saying that Kashgari had been repatriated and that the charges against him would be decided by Saudi authorities. "Malaysia has a longstanding arrangement by which individuals wanted by one country are extradited when detained by the other," he was quoted as saying.
Blasphemy is a crime punishable by execution under Saudi Arabia's strict interpretation of Islamic sharia law. It is not a capital crime in Malaysia.
Reuters could not verify Kashgari's comments because he later deleted them, but media reported that one of them reflected his contradictory views of the Prophet - that he both loved and hated him.
Kashgari later said in an interview that he was being made a "scapegoat for a larger conflict" over his comments.