The disclosure of the missing funds and complaints of criminality come just ahead of the airport's long-scheduled presentation of annual financial results tomorrow.
Market analysts are picking the result for the 2015 financial year to be positive, with Morningstar suggesting ongoing growth in tourism would see revenues this year exceed $500 million and profits tipped to be $328 million.
The airport case comes as two other former employees of large listed companies find themselves facing court action this week over claims they misappropriated millions of dollars of employers' money.
Paul Kenneth Rose, a former electrical engineer at Mighty River Power, is currently on trial at the High Court at Auckland facing four charges of obtaining $2.3 million by deception.
The offending allegedly took place over his eight years of employment at the power generator which only ended after he was dismissed following an investigation in December 2012.
Rose has pleaded not guilty to charges he abused his position by buying and marking-up parts and equipment he would then on-sell to Mighty River Power.
SkyCity is chasing Tessa Grant through the High Court for $1.27 million after uncovering alleged fraud.
The casino operator reviewed Grant's activities as a senior manager at its Hamilton casino between 2006 and 2014, after she pleaded guilty last year to defrauding Waikato Diocesan School for Girls of almost $800,000.