"Action has been taken and the systems are now secure," he said.
"There is no evidence any of these weak points led to a breach of privacy or information security."
One of those was at privately-run Mt Eden prison, where inmates were temporarily able to access the internet late last year. "No email, social media or adult sites were accessed," Scott McNairn of prison operator Serco told the Herald.
Prisoners had "limited" internet access for about 12 hours but that was "policed by a web filter which blocked access to inappropriate sites".
Other departments where weaknesses were identified included the Ministry of Social Development again, and the Ministry of Justice.
However, Mr MacDonald acknowledged the "desk-based" review of documentation around IT security probably didn't detect all weak points.
"All agencies are now obliged to do a complete risk review of their publicly available systems ... Until those agencies do the detailed risk assessment ... in the next few months, there could still be further vulnerabilities."
Prime Minister John Key has downplayed the seriousness of recent privacy breaches, including the EQC email blunder this year, saying they didn't indicate "systemic" problems with private data handling by government departments but Privacy Commissioner Marie Shroff yesterday offered a conflicting view.
It was "a wake-up call to the government sector" she said. "It reveals systemic weaknesses in the way privacy and security have been managed." She welcomed Mr MacDonald's recommendations, particularly that information security issues were overseen at senior management level, rather than leaving that work to IT staff and contractors.
Labour Leader David Shearer said Mr Key had sat on Mr MacDonald's "damning review", while downplaying the seriousness of privacy breaches.
He said Mr Key received the report late last year but three months later, "flatly denied there was a systemic failure across government, arguing that privacy breaches were inevitable and that 'from time to time people make mistakes'.
"That's deliberately misleading. He had the information and he chose to tell the House and New Zealanders whose private information is held by these agencies the opposite of what he knew to be true."
Failed report card
• Government Chief Information Officer Colin MacDonald and KPMG reviewed 215 public-facing IT systems across 70 government departments and found:
• 12 departments had "weak points" or specific vulnerabilities
• 73 per cent of agencies didn't have formal information security risk management processes
• 67 per cent of systems had not undergone a security assessment
• 82 per cent of systems did not have detailed security design documentation