Auditor-General Grant Hehir said in the Australian National Audit Office annual report that there were some concerning trends towards greater secrecy of government information.
"I have observed increasing complexities associated with auditing in a contestable environment, specifically the shift towards government and service provider information being held not only as commercial-in-confidence, but at increasingly higher levels of security classification," Mr Hehir wrote in the report released on Thursday.
"There have also been more issues being raised regarding the protection of personal information. Impediments, or perceived barriers, to this access represent a challenge to the audit process."
He said the role of the auditor would always be focused on transparency and providing the information necessary to assist the parliament in holding the executive arm of government to account.
"The efficient collection of sufficient and appropriate information - to form substantive, accurate, evidence-based conclusions - is critical to our work," he said.
"Preserving and refreshing the auditor-general's information-gathering powers in the shifting environment of the public service remains a key issue for the ANAO."
Mr Hehir highlighted "deficiencies" with cybersecurity in government departments and agencies, procurement processes lacking "value for money", and poor grants administration as key areas of ongoing concern.
"The ANAO's audit work has shown that advice to government (on grants) has not always been robust - including insufficient attention to the authority of decision-makers and poor record-keeping in decision-making without assessment, or rationale for decisions being documented."
Mr Hehir welcomed extra funding for his office in the 2021/22 budget which would enable it to hit a target of 48 performance audits by 2024/25.