About 1000 police files were found at the premises, which include one with direct links to bikies, he said.
Mr Lay said the scale of the discovery was shocking for the organisation.
The vast majority of people mentioned in the documents were people with long criminal histories and some had already been visited by police to ensure they are not hurt, he said.
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"The good thing about this is, every one of these documents, we can actually follow the order trail and understand when, how and who actually had access to them so that is of some comfort," Mr Lay told 3AW today.
"The overwhelming feeling in the organisation at the moment is that there has been a gross betrayal of the organisation, of the community and of the colleagues close to this person that has undertaken this act."
He said there were two very high risk matters that police needed to get on top of very quickly and he believed they had done that.
"We just do what is called a risk assessment and we work our way through what the best way of keeping these people safe is," Mr Lay said.
He said the documents were printouts from the LEAP database and other police systems and they went back nearly three years.
The chief commissioner said the person should not have had access to the data, but used a method to access it that prevented people from knowing.
"Obviously someone has taken a fairly proactive approach to collecting a whole host of data around particular people," Mr Lay said.
He said there had been discussions with the director of the Independent Broad-based Anti-corruption Commission, but police were investigating the matter.
A junior officer at the centre of the leak scandal has been suspended without pay and is likely to be charged, police said on Monday.
Mr Lay said on Monday the leaked documents put the lives of police and members of the public at risk.
heraldsun.com.au 9 May 2013
A motion of no confidence should be made with regards to the corrupt dealings of the organisation known as Victoria Police.
Corruption from the top dogs of 'Vicpol' has been going on for decades, and only now the surface is being scratched.
One cannot rely on the reporting of corruption from the source of the corruption, especially since previously Victoria Police has shown that it has falsified crime figures.
A truly independent body should be carrying out the investigative work.
Victoria Police also works together with members of the masonic brotherhood, to eliminate all sorts of traffic infringement notices all the way up to criminal offences in high courts.
Victoria Police is one of the more corrupt organisations set up by a corrupt Australian 'government'.
Stand up to those pricks...
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