It said in a statement that Madonsela told a workshop organised by two portfolio committees that some oversight structures had incomplete mandates and may not have the power to remedy administrative wrongs or conduct failures.
The committees were for justice and correctional services, and for women in the presidency.
Madonsela gave an example of whistle blowers left in limbo for 10 months since October 2013, with one out of work since December.
She said she referred the complaint to the Public Service Commission (PSC) which indicated that they have no jurisdiction to investigate.
The complaint was then referred to the Special Investigations Unit (SIU) whose proclamation was signed but withheld. There has been no investigation on the matter to date, she said.
She explained that the National Development Plan (NDP) recognised overlaps and noted cracks and poor co-ordination.
The NDP further recommends strengthening through resourcing, improved co-ordination and respect of her office, Madonsela said.
She said that even though overlaps were impossible to eradicate since her office operates within a multi-agency oversight structures, the focus should be on preventing duplication.
Madonsela said what was important was not to start investigations when another structure was already investigating.
She reiterated her appeal for adequate resourcing to help her office live up to its constitutional mandate, which required it to be accessible to all people and communities.