The Department of Home Affairs will not issue temporary passports from next month.
Department spokesman Mayi-hlome Tshwete said the temporary passport s were being withdrawn because the turnaround time for issuing permanent ones had improved and because temporary documents had been used fraudulently.
"A lot of other countries are also moving away from manually to digitally issued passports," Tshwete said.
The department has introduced a system that can digitally issue a passport within 13 days. It takes 24 days if entrusted to people.
For emergency travel an emergency certificate can be issued within a day.
Tshwete said all countries accepted South African emergency travel certificates.
The UK, Germany, The Netherlands, Belgium, Luxembourg and Canada, according to the Department of International Relations and Cooperation, are among the countries that do not accept South African temporary passports at ports of entry.
Over the past decade South African passports have been used fraudulently by terrorist organisations and other criminals.
The Institute for Security Studies said the South African passport is popular among criminals because of the ease with which passport application documents, such as birth certificates, can be illegally obtained.
Samantha Louise Lewthwaite, also known as the "White Widow", used a fraudulently obtained South African passport.
She is wanted by several countries for terrorist activities.