The move follows allegations from construction unions that contractors are not sticking to employment terms and conditions agreed with the Olympic Delivery Authority (ODA).
Main groundwork contractor Nuttall has instructed the KPMG team to probe the unions' claims.
The auditors will look at working practices and conditions and how labour is recruited on the site.
One union source said: "The Games' organisers have committed to fair employment practices so we need to check that is happening.
"We need to know things like all contractors and labour suppliers are signed-up with the industry holiday pay scheme. There has also been talk of agency workers having excessive deductions from their pay."
A Nuttall spokesman said the audit had not discovered any evidence to back-up union claims and that nobody had been removed from the site in relation to the probe.
He said: "There are always a lot of allegations flying around on a job like this where there is a lot of politics involved.
"We decided it was a good move to get an external auditor to examine working practices because its report will carry more weight than an internal investigation."
An ODA spokesperson said: "As part of our shared commitment to fair employment on the Olympic Park we work closely with our contractors and the construction trade unions to ensure the agreed standards are being met. This includes ongoing employment audits and a swift response to immediate concerns raised.
"We have been working with Nuttall to investigate this particular issue, alongside an internal audit being carried out by the contractor, and to date no evidence to support the allegations has been found."