Chief Executive of Metro Trains Raymond O'Flaherty said on Friday he had given notice to Transclean that its agreement was being terminated and a new cleaner sought.

The move comes after the last day of public hearings for the Independent Broad-based Anti-Corruption Commission's Operation Esperance about alleged misconduct relating to Melbourne's trains.

The investigation has revealed carriages were not cleaned properly during the city's first wave of coronavirus, an issue Mr O'Flaherty said would be rectified with a new cleaner.

Transclean managing director George Haritos was questioned for a second time on Friday at IBAC and repeatedly denied all wrongdoing, even after listening to damning tapped phone calls with Metro Trains manager Peter Bollas and V/Line chief James Pinder.

Counsel assisting the commission Paul Lawrie put to Mr Haritos that he had been making monthly cash payments of between $8000 and $10,000 to both men.

"From early on when Mr Pinder was working at Metro you became very good friends with him and subsequently you came to know Mr Bollas," Mr Lawrie said.

"The three of you commenced an arrangement which involved secret cash payments from Transclean back to both Mr Bollas and Mr Pinder."

Mr Haritos replied that he could not have made a profit for Transclean if he made such payments.

Numerous phone calls were played throughout the hearings detailing Mr Haritos' arrangements with other people to transfer cash to the men, but when questioned he would say the money was for a granddaughter, his elderly mother's care or a loan for an employee.

He often forgot the question he had just been asked, could not recall basic facts or would dismiss what was said in a phone call as a joke.

In one July phone call about the ongoing cost of the cleaning contract, Mr Bollas asked Mr Haritos if there would be "any honey" for him.

"Not honey, sprinkled," Mr Haritos replies.

Mr Lawrie put to the commission that Mr Haritos moved money to Mr Pinder through friends by making it look like a personal loan.

"You disagree with that of course," Mr Lawrie said.

"Of course I do," Mr Haritos replied.

"The reason you were paying James Pinder that money in addition to what I say is his usual monthly retainer is as a reward for him championing your cause so that Transclean won the V/Line contract. This was his pay-off.

"Totally wrong," Mr Haritos said.

"Transclean won the V/Line contract purely on its merits."

Metro Trains and V/Line have severed ties with Peter Bollas and James Pinder respectively, and V/Line ended its contract with Transclean last week.

Mr Pinder is alleged to have pocketed $320,000, including a $100,000 loan for the deposit on his Williamstown home, to further the interests of Transclean.

Mr Haritos has defended Transclean's cleaning performance, saying the company did a successful job given that no coronavirus cluster arose from infection within a train.

Australian Associated Press