The confession was therefore discredited as a piece of evidence in the murder case against Aliyev. "According to the report it is assumed that the confession is a forgery," said spokeswoman Nina Bussek.
The controversial document was obtained as the result of a search of Aliyev's residence.
The confession admits to participation in the murder of the two Kazakh bankers who worked for the bank of which Aliyev was a part owner.
The Austrian federal prosecutor requested the testimony of a professional graphologist, who has submitted in a report that the handwriting is unlikely to belong to Aliyev.
Nevertheless, the prosecution maintains it has a strong case against the former ambassador. "The firm suspicion is based on additional evidence," said Bussek. Some of that additional evidence includes an intercepted Skype call, which undermines his alibi for the murders.
Aliyev is the former son-in-law of autocratic ruling Kazakh President Nursultan Nazarbayev. He fell out of favor and was sentenced in 2008 in absentia for murder.
Austria has twice refused extradition requests from Kazakhstan because of concerns about the rule of law and the fairness of the trial in the Central Asian former-Soviet republic.
Therefore, the Austrian justice department has decided to conduct its own investigation into the murders, as well as a related case of money laundering.
The Vienna public prosecutor issued an arrest warrant for Aliyev in May. Aliyev, who was living with his Austrian wife in Malta, was arrested when he returned to Austria in June.
Aliyev is currently awaiting trial in an Austrian prison, where his lawyer has claimed he is being subjected to threats, extortion and intimidation.