Pretoria - Home Affairs says the passport found on a dead al-Qaeda member in Somalia was not an authentic South African passport.
Following investigations, the department's DG Mkuseli Apleni confirmed on Wednesday that the fake passport was based on the previous passport design and not on the new one.
"Our investigations have revealed without equivocation that the passport was not an authentic South African passport, but a fake," Apleni told a media briefing.
He said the passport had also not been issued by any South African authority and there was no record of the passport being used to enter or leave South Africa.
Media reports have indicated that the passport found on Fazul Abdullah Mohammed, who was shot dead by Somali government forces at a roadblock in Mogadishu last Wednesday, had a recent exit stamp from SA.
Fazul was reportedly carrying a South African passport under the name Daniel Robinson - giving his year of birth as 1971.
He was the alleged mastermind of the 1998 US Embassy bombings in Kenya and Tanzania and was also suspected of plotting the Kampala bombings a year ago by al-Shabaab. The bombings in Dar es Salaam and Nairobi killed 224 people.
He is also believed to have been the mastermind of an attack on a hotel along the Kenyan coast in 2002 that killed 15 people.
"The South African Movement Control System has no record of any Fazul using the fake passport at any entry of out points of entry," said Apleni .
Modiri Matthews, head of the immigration inspectorate at the department, said Fazul faked the old South African passport, but it was still visible that it was not genuine.
Matthews says the colour, background, font and spacing, among other things, were completely wrong.
The department is also introducing an online fingerprint verification system that will eliminate the role of third parties in the application and collection of passports.
The two officials said the new high-security passport introduced last year would make it even more difficult for criminals to fake.
The new passport contains several security features that are tamper-proof, making it impossible to forge.
Apleni said the online fingerprint verification system would be used to confirm the identity of the applicant as well as to minimise risks of identity fraud.
"The systems that government has put in place, such as the Movement Control System, are effective and efficient and will continue to assist the country in its efforts to push back the frontiers of fraud and corruption."
The department will also continue to work in collaboration with other law enforcement agencies to protect the integrity of SA documents.