Poaching syndicates have penetrated the department of fisheries, corrupting some officials, Fisheries Minister Tina Joemat-Pettersson revealed on Wednesday.

"A preliminary investigation reveals that there is corruption within our fisheries branch in the department, and that some officials may be implicated," she told reporters at Parliament in Cape Town.

The investigation was "sensitive and at an advanced stage", and had initially focused on perlemoen poaching.

However, there was also corruption "in the allocation of quotas, permits, transfer of rights and preferential treatment given to certain businesses".

An internationally-recognised auditing firm had been engaged to carry out a forensic audit at the fisheries branch. This move appears to have triggered a fight back by the syndicates.

Joemat-Pettersson warned attempts were being made to "destabilise" her department.

"There's an attempt at destabilising the department, and this... will not be tolerated. There's also been all sorts of information surfacing about me as a person... but I will not be intimidated or harassed. This investigation will continue."

The efforts to destabilise her department were both "internal and external", she said.

Several witnesses had been placed in the Witness Protection Programme.

"There is a threat to some people's lives."

Referring to the perlemoen poaching syndicates, Joemat-Pettersson said they were "not a good group of people" to tangle with, being linked to the drug syndicates.

"They [the syndicates] have influenced a number of people in my department," she said

Referring to the spate of arrests involving perlemoen poachers in the Western Cape in recent weeks, Joemat-Pettersson also suggested these were linked to the ongoing investigation.

Such arrests "did not happen automatically", she said.

"As you can imagine, if you investigate one person, it opens a hornets' nest".

Tens of thousands of individual perlemoen have been confiscated by fisheries officials and police over the past month.

The minister declined to say how many officials were implicated in corruption.

"But if you look at the [quantity] of abalone we have confiscated, then you can imagine what the extent of the investigation will be like," Joemat-Pettersson said.

The investigation was being conducted at "very high, senior levels" and involved the police, state intelligence agencies, the SA Revenue Service, the SA National Defence Force and the SA Navy.

She said there would be more arrests.

"What we've seen [so far] is the tip of the iceberg."