"We believe there was more money, some of that money is no longer there," he told reporters.
Katsogiannis said the alleged fraud was at "the top echelon".
The second executive, a US national who police allege was trying to flee the country when he was arrested, is accused of being in a corrupt relationship with an overseas company that was providing IT services to the CBA.
The man was allegedly receiving kickbacks from a not-for-profit organisation, set up as a shell company to launder the payments from the US-based IT company.
Police allege the two executives granted the IT company a lucrative contract without putting it to public tender and in exchange the managers received kickbacks.
The US national was fired from the bank late last year. He is charged with two counts of bribery.
The two individuals, who were already on substantial salaries, were probably the most senior executives that have been caught out for this offence, Katsogiannis said.
The bank contract awarded to the company was worth tens of millions of dollars, police allege.
A Commonwealth Bank spokesperson confirmed it was the institution that reported the matter to police.
"We have no tolerance for illegal activity by any employee and we take every situation seriously," the spokesperson said.
"We confirm that no customer has been affected by this matter."
- AAP