The State Security Agency (SSA) and Parliament's joint standing committee on intelligence are drafting new regulations around vetting procedures at State institutions that will include sanctions.

State Security Minister Bongani Bongo and SSA Director-General Arthur Fraser addressed the Standing Committee on Public Accounts (Scopa) on Thursday on the vetting processes at government departments.

A coy Fraser said he could not give much detail away about the drafting of the new legislation, but said it would ensure greater consequences for non-compliance.

"These regulations should be finalised very soon. There is just one element we are [still] finalising," he told MPs.

"The regulations are going to attach a sanction to both the individual and the head of the institution. That is important going forward."

Bongo agreed, saying that although accounting officers already had powers to vet individuals, accountability was a problem.

"What was lacking is the sanction. In the main, we want to zoom in on sanctions to the accounting officer and the one who does not want to take polygraph-related assessments.

"We also accept we have not moved at the pace that Parliament has wanted us, but we are a nation at work."

The meeting was called after it came to light that only 7% of Transnet's supply-chain management (SCM) staff have been vetted, despite a 2014 Cabinet instruction that all SCM staff in government be vetted.

Scopa MPs appreciated the developments, but said the nitty-gritty of how they conducted vetting was between them and the standing committee.

What was of concern to Scopa, was that it was leading to small and huge rand losses at almost all levels of government through corruption.

"Supply-chain management is the playground of corruption, and staff have not been vetted, despite Cabinet's decision," said Inkatha Freedom Party MP Mkhuleko Hlengwa.

"That is the biggest threat to national security at the moment; freeloaders dealing with public funds. We need to plug the hole."

African National Congress MP Ezekiel Kekana said it was worrying that the SSA seemed to be explaining away the lack of compliance on Cabinet's directive.

Democratic Alliance MP David Ross said heads of state institutions also had a duty to vet individuals, and that the SSA should ensure compliance.

Fraser admitted that there had been little follow through on Cabinet's instruction, but claimed the problem was one of resources, volume and time. The process was also still manual, he said.

They also found resistance from some top executives and labour unions.

"We are vetting, we just aren't doing enough. We have found in many instances that people do not want to co-operate or be a part of polygraph tests."

The solution, he explained, was a proposed e-vetting system for the first two phases of the process, including the gathering of information.

A pilot run of a new digital system is planned for April 2018.

"We will enroll all individuals who do business with [the] State and verify their bona fides. Once we have digitised and modernised our vetting, we'd be able to reflect on all those that work within the State.

"It would then mean we can do more detailed investigation when required."

Up until now, heads of state institutions could still override an SSA recommendation and appoint an individual without a security clearance, he said.

The legislation and the new system would deal with the workflow problems and ensure sanctions in future.

They were also in the process of placing a unit within the Chief Procurement Office at Treasury.

Hlengwa ended with a warning around Cabinet's directive.

"If that is not done with the necessary haste, then we can come to no other conclusion than that the SSA is aiding and abetting non-compliance in the SCM sector and the rise in corruption.

"It makes you complicit."

After the meeting, Bongo told two journalists that he had not yet received any feedback from his political authority or the police over accusations that he had tried to bribe the evidence leader of Parliament's Eskom inquiry.

He said the matter was sub judice and he could not comment, before being whisked away by four bodyguards.