Three agencies with powers to investigate and audit the bureaucracy have warned a national integrity commission model under Senate scrutiny could undermine inquiries, duplicate their work, force breaches of parliamentary protections and stumble into intelligence operations.

The scramble among watchdogs to protect their jurisdictions and independence, in response to a crossbench bill to create an integrity commission, could also raise problems for the government as it proposes a model with similar features.

Australia's Inspector-General of Intelligence and Security, which monitors spy agencies, told senators the model proposed by crossbenchers could raise national security "implications" and risked overlapping its jurisdiction.

Inspector-General Margaret Stone said the integrity commission laws, which would compel government officials to report possible corruption, could force intelligence agency heads to reveal ongoing security investigations and activities to the new watchdog.

The model could also inadvertently capture spies properly performing their duty but relying on immunities from legal liability, she said.

Plans to compel public servants to report wrongdoing could undermine the Inspector-General's oversight of spy agencies by creating a "chilling effect" stopping them telling her of their operations, Ms Stone said.

Strict secrecy laws also prevented the Inspector-General giving information to law enforcement agencies and courts when it was gathered under legislation creating her office.

"Rather, if IGIS identified information which suggested the potential commission of an offence by an individual, IGIS would inform the relevant agency head, or in some circumstances police," she said.

Ms Stone questioned the proposed integrity commission's ability to investigate intelligence officials and others with access to classified information.

"IGIS is a specialised oversight agency that is equipped to deal with managing highly classified information," she said.

"Officers reviewing intelligence agency activities have the highest level of security clearance and the office space and equipment used by IGIS staff is accredited in accordance with the relevant security standards.

"The difficulties and cost of replicating this ability to deal with highly classified information in a new agency should not be underestimated."

The Australian National Audit Office suggested the proposed legislation creating the new body could undermine parts of the federal government's broader regime of oversight keeping public officials in check.

The agency said it was unclear if the proposed watchdog could stop its audits, which uncover waste, department failures and incompetence in large-spending government projects.

It urged changes to the model, saying it should exempt the office from handing over documents gathered in audits or giving evidence relating to an audit.

The integrity commission could otherwise force the audit office to break laws by giving it information gathered before the auditor could report to Parliament.

Instead, the agency proposed it could pass information on to the integrity commission if it decided it was in the public interest.

"Preservation of the Auditor-General’s independence in this respect would further strengthen the proposed integrity framework," it said.

The Inspector-General of Intelligence and Security, the audit office and Commonwealth Ombudsman Michael Manthorpe wanted laws to make clear the integrity watchdog could not direct them to investigate cases and compromise their independence.

The Ombudsman, which receives complaints from members of the public about government agencies and their decisions, said the crossbench bill could duplicate its work in creating a parliamentary inspector overseeing the integrity commission. Mr Manthorpe proposed giving the inspector role to his office.

"This would obviate the need for a further proliferation of integrity-related bodies. Alternatively, further drafting could be commissioned to differentiate the respective roles of the parliamentary inspector and the ombudsman," he said.

The Coalition's proposed model for a Commonwealth Integrity Commission suggests it would receive referrals from the Ombudsman, the Auditor-General and the Inspector General of Intelligence and Security, but does not say if these would be mandatory.

It would also create a new offence covering senior officials who failed to report public sector corruption. The commission's division covering non-law-enforcement public servants would have the power to question them, and compel them to hand over documents.

Senators will hold a hearing into the crossbench's proposed integrity commission on Friday in Sydney, and are due to report in April. The federal government, which released its own proposal in December, is yet to decide its final model and finished receiving submissions last week.