Mkhwebane also praised her subordinates for their hard work under "extremely difficult conditions".
"… they have outdone themselves. It is going to be important to maintain and build on these successes, going forward. As an integrity institution, we are held to a higher standard than the average organ of state. We must lead by example," she said.
In a statement released by her office on Wednesday, it claimed that it had slashed irregular expenditure by R16m while incurring no new irregularities in expenditure during the 2018/2019 financial year.
The Chapter 9 institution posted a surplus of R19.2m compared to the previous financial year, when it reported a R19.1m deficit.
The institution claimed only one transaction valued at R2 400 was red-flagged as fruitless expenditure from R1.4m.
Goods suppliers were also paid within 20 days of invoicing.
With a budget of more than R311m and 346 employees nationally, the Office of the Public Protector had issued 46 formal investigation reports, which were 16 more than its target and finalised 99% of its caseload within specified time frames, she said.
"It also managed to finalise 77% of aging cases of two years and older. All in all, 9 912 out of a total workload of 14 147 cases were finalised. In 46% of the finalised complaints, the allegations were confirmed while that was not the case in 36% of the cases."
Mkhwebane said 17% of cases were finalised without investigations.
"This would be in instances of non-jurisdiction matter," read the statement.
The Department of Home Affairs and municipalities accounted for the bulk of complaints received by her office, followed by the Department of Justice and Correctional Services.
The departments of education, labour, health and human settlements as well as the police, Government Pensions Administration Agency and Sassa completed the top 10 of institutions that complaints were brought against.
Mkhwebane said more needed to be done to take the services of her office to grassroots level and positively impacting the lives of ordinary people who see her office as the only avenue they can hold their elected leaders to account.
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