The controversy over the tweet is that he insulted Prophet Muhammed in his. Prophet Mohummed is most dearly loved and respected by Muslims all over the world. Any comment against him naturally angers them.
Police confirmed to the BBC that Hamza Kashgari was sent back to Saudi Arabia on Sunday despite protests from human rights groups.
Insulting Prophet Muhammed is punishable by death in Saudi Arabia.
Mr Kashgari, 23, fled Saudi Arabia last week and was detained upon his arrival in the Malaysian capital Kuala Lumpur on Thursday.
He had tweeted his doubts about Muhammad on the prophet’s birthday last week. Saudi clerics condemned his remarks as blasphemous.
Mr Kashgari apologised and deleted the tweet, but when he continued to receive threats, he left for Malaysia.
“The nature of the charges against the individual in this case are a matter for the Saudi Arabian authorities,” Malaysia’s home ministry said in a statement.
Amnesty International has warned that Mr Kashgari could be executed in Saudi Arabia if he is found guilty of apostasy.
“If the Malaysian authorities hand over Hamza Kashgari to Saudi Arabia, they could end up complicit in any violations he suffers,” said Hassiba Hadj Sahraoui of Amnesty’s Middle East division.