The police's Crime Intelligence Unit was infiltrated, national police commissioner Lieutenant-General Khehla Sitole admitted.
He and crime intelligence head Major General Peter Jacobs presented a Crime Intelligence's turnaround strategy to the Portfolio Committee on Police on Wednesday.
DA MP Zak Mbhele asked whether the factionalism in the unit was purely due to internal organisational dynamics, or whether it was being co-opted into an external political faction.
ANC MP Leonard Ramatlakane asked, also in relation to the factionalism, whether everybody accepted the "new order".
"What we can confirm is that Crime Intelligence was infiltrated. I don't want to use another word," Sitole said.
He did not elaborate or say who infiltrated it.
He said they "worked on the purification" of the unit.
The police are apolitical, Sitole said.
"As SAPS we're not affiliated to any party. We arrest criminals," he said.
He said the new order is being accepted. He said when they appointed Jacobs in March, he was ordered to command the unit, and if he failed, he would have to get out. He said this order was extended to everyone in the unit: "Accept it or ship out."
"The rogue units were closed down," Sitole answered, to a question on whether there are still rogue units in Crime Intelligence.
Sitole described the damage that was done to the unit as severe.
"When the damage was severe, you cannot repair it in one day," he said.
He said the unit got caught in an "under-budgeting backlog". He said this will be addressed by the business case the police force is taking to Cabinet and the Treasury.
There will be a special focus on increasing CI's technological capabilities.
"The technology capability of CI is far from matching the technology advancements of criminals," said Sitole.