National Prosecuting Authority (NPA) boss Menzi Simelane on Wednesday said that the reporting lines of specialised prosecution units have changed, raising questions about whether he respected ministerial orders to suspend a restructuring plan.

Simelane told Parliament's portfolio committee on justice that the specialised units - including the Specialised Commercial Crimes Unit (SCCU) - were now also reporting to deputy directors of prosecution.

He denied a charge from the opposition that this amounted to disbanding the four units in the NPA that have won plaudits for their high conviction rates and also include the Asset Forfeiture Unit (AFU).

"The issue around restructuring was one not about whether or not there was a disbandment. It was about who people report to," Simelane told MPs.

He said that the units were told to report to regional structures because by law deputy directors of prosecution must be able to account for every case heard in their jurisdiction and therefore cannot be in the dark about "complex crimes matters because people report elsewhere".

"In the strategy we reflected that reporting line, that is what the restructuring was about not whether any unit is being disbanded."

Simelane first unveiled his plans to decentralise the functioning of the units in April, with his staff saying the level of autonomy enjoyed by the units, notably the AFU, had become untenable.

It caused an outcry and Justice Minister Jeff Radebe claimed that he had been left in the dark about the plan.

He ordered any restructuring to be put on hold until the government had concluded a performance contract with the justice and security cluster. Unhappiness about the plan, and about Simelane's appointment as head of the NPA, escalated when it emerged that the head of the SCCU, Chris Jordaan, had been demoted.

Jordaan was subsequently reinstated and President Jacob Zuma assured the National Assembly that "any restructuring of the NPA has been deferred".

Simelane referred to Jordaan on Wednesday, and said that his position had in no way been compromised by the new reporting protocol.

"So the scenario as it stands now, is that Chris Jordaan who is a special director in the office of the NDPP (national director of public prosecutions) is still the head of the SCCU.

"Various heads in the DDP offices do submit reports to the offices of the NDPP for Chris to have a look at but I have further instructed them to submit reports to the DDP office.

"So they have one solid line and one dotted line until such time then that a final decision gets made on this point."

Simelane said that he was still waiting for Radebe to decide whether the NPA's five-year restructuring plan would go ahead.

"We are still waiting for the minister to make that decision. But on the ground how it works is that everybody works together anyway because that has to happen."

Democratic Alliance justice spokesperson Dene Smuts said it appeared that Simelane had defied Radebe and pushed ahead with the plan.

She said that she would write to the minister to bring the matter to his attention.