Mr Brownlee said Cera was subject to annual audits, including quality assurance reports, as well as a robust select committee process, and was assisted in financial management by Treasury.
He said he remained proud of the work Cera staff accomplished alongside other local and central government agencies, and staff should be as well.
Cera was set up to lead and co-ordinate the recovery from the 2011 Canterbury earthquakes and was dis-established last year, with its roles transferring to others.
Auditor-General Lyn Provost said Cera did well early on.
It was effective in managing the demolition of condemned buildings and in leading a co-ordinated government response to the earthquakes. But it found it challenging to maintain momentum.
Its role became less clear as it took on more responsibility for delivering more projects and programmes.
The report is the last in a series by the Auditor-General on the Canterbury recovery.