The NPA's report, presented to Parliament's justice portfolio committee on Tuesday, also showed there were 754 convictions on complex commercial crime; 1 525 for the trio crimes, 171 for organised crime and 4 501 for sexual offences.
"These include all sexual offences, not necessarily the traditionally defined sexual offences, which do not necessarily have to have penetration," acting NPA head Nomgcobo Jiba said.
The document also revealed there were 6 125 criminal court cases in which a sentence of 10 years or more of direct imprisonment without the option of a fine was imposed.
The number of backlog cases stood at 17 646 for the 2011/12 financial year.
In a statement, the Democratic Alliance (DA) criticised the NPA for the "shockingly low number of sexual offences being finalised".
DA spokesperson on justice, Debbie Schafer referred to the figures as "a national disgrace", adding that Justice and Constitutional Development Minister Jeff Radebe "should hang his head in shame at his failure to give this matter the attention it deserves".
"The report has shown a shockingly low number of sexual offences cases being finalised, and even fewer resulting in a conviction," she said.
In the same paragraph of the annual report in which the NPA described how it was enhancing its focus to protect the rights of vulnerable groups, it stated that only 6 913 sexual offence cases were finalised in 2011/12.
"The conviction rate of these cases was only 65.1%," said Schafer.
She said considering the fact that 64 415 sexual offences were reported to the police in 2011/12 means only 11% of reported cases were finalised and only 6.9% – or 4 500 – actually resulted in a conviction.
Schafer added that at 60.7%, conviction rates were considerably higher for cases reported at Thuthuzela Care Centres, which are one-stop centres for survivors of sexual offences. But the conviction rate for these centres also declined, from 63% to 60.7%.
One of the reasons listed for this decrease was the "substantial drop" in dedicated courts.
Jiba said the state maintained a high conviction rate in all courts in 2011/12, with an overall conviction rate at 88.8% of all crimes.
The NPA planned to finalise 365 087 cases over the financial year, but fell short of this target as only 316 098 cases were finalised.
This was due to a steady decline in court utilisation and increase in formal bail applications, she said.
But the NPA exceeded its target on the number of cases finalised through alternative dispute resolution mechanism.
Improved court efficiency
Jiba told the committee that in previous years there seemed to be a lack of cooperation from the judiciary, "but I must say right now there is a lot of commitment to ensure that court efficiency is improved".
She said a meeting chaired by Chief Justice Mogoeng Mogoeng was held on Saturday to address issues relating to court efficiency.
The result was the formation of a committee, which would look at measures or indicators to put in place to bind "us all" to ensure courts were performing well.
"We are also trying to identify priority courts where there is a [high] volume of work and we will pump more resources … We have acknowledged that our main problem is finalisation of cases with verdict," said Jiba.