In documents filed in the Victorian Supreme Court in support of the freezing order, Coles accused Mr Baslangic of making $1.93 million in "questionable transactions" to accounts and entities outside of the company.

Coles said it identified the transactions in late July as it prepared to move to a new payment system.

The head of Coles' fraud protection team, Cameron Newell, said in an affidavit dated July 30 that he was investigating 13 payments, which ranged from between $52,532 to $304,319.

Mr Newell said the payments were flagged as suspicious for several reasons, including that some did not have invoices, or had invoices that were sent from Mr Baslangic's personal email address.

Six transactions above Mr Baslangic's $75,000 approved transaction limit were submitted with emails appearing to show Coles Online's general manager Karen Donaldson clearing the payments.

However, Ms Donaldson submitted to the court that she had not approved the transactions and believed the emails had been "falsified".

Mr Baslangic started work at the $18 billion retailer's head office in Melbourne in 2014 and moved through several financial roles, according to his LinkedIn profile.

He was released on bail and is due to appear at Melbourne Magistrates' Court on Tuesday.