She said trusts that reported breaches as part of the commission's annual healthcheck were to be 'applauded'.
Nearly one in three trusts failed to fully comply with the hygiene code in 2006-07, the annual healthcheck found.
Patients' records were not managed systematically by 18 per cent of trusts, while 65 trusts had not ensured their staff attended mandatory training.
However, overall 6 per cent more trusts than last year believed they met all standards.
Ms Walker said: 'We want to applaud trusts that have put their hands up and declared non-compliance in some areas. This shows boards really examining their own performance.
'That is the action of an honest and responsible board that wants to make improvements and get these standards in place for patients.'
But she warmed that where trusts have declared significant non-compliance, the Healthcare Commission will contact strategic health authorities.
'We will come down harder where we find non-compliance in practice,' she said.
'That is why we will ensure rigorous analysis of the accuracy of what organisations are saying, using the array of data we hold and targeted inspection where necessary.'
Random spot-checks will be followed by an official performance rating, to be announced in October.