Commonwealth Bank has been hit with another 100 allegations of breaches of anti-money laundering and counter-terrorism laws, including failing to quickly report two suspicious matters relating to the financing of terrorism.

The Australian Transaction Reports and Analysis Centre (Austrac) filed an amended statement of claim to the federal court on Thursday. In it, the federal government’s financial intelligence unit updated the total number of alleged breaches by Australia’s largest bank to more than 53,800.

Among the latest allegations are that CBA failed to report terrorism financing suspicions within 24 hours, was either slow or negligent in reporting 54 suspicious matters relating to accounts or people under law enforcement investigation, and in 38 instances did not appropriately monitor risk, even after becoming aware of suspicious activity.

The statement of claim now includes alleged breaches from as early as December 2011, rather than May 2012 as in the original claim.

The chief executive of Austrac, Nicole Rose, said the additional alleged contraventions were identified after civil penalty proceedings were first initiated in August.

“These allegations are very serious and reflect systemic non-compliance over approximately six years,” Rose said.

The maximum penalty for each alleged contravention in the amended statement of claim is $21m.

CBA shares fell as much as 1% in the first few minutes on Thursday, hours after the lender said it expected fresh allegations, but had rallied to sit 0.1% higher at $80.39 by the afternoon.

Late on Wednesday the bank filed its defence to Austrac’s initial allegations – made in August – admitting it was late filing 53,506 reports on transactions due to a systems error and that it did not adequately adhere to risk assessment requirements for automated deposit machines.

CBA shares shed about 14% of their value over the five weeks immediately after Austrac alleged the bank had failed to properly monitor potentially suspicious transactions.

In that period CBA announced that its chief executive, Ian Narev, would retire and executives would not receive their short-term bonuses.

The bank argues that its failures should not amount to separate contraventions of the law, which would dramatically reduce any potential fine.

It has admitted to 91 of 174 of Austrac’s original allegations that it failed to properly submit suspicious matter reports (SMRs), and will argue that many of those relate to reports that were missing specific transaction details and should not result in a civil penalty.

The bank will also argue it lodged a significant number of SMRs related to the customers highlighted in Austrac’s allegations and that this should be considered when the court assesses the harm caused by CBA’s failure to comply with all the legal requirements of those reports.

“During the period of the claim, CBA submitted more than 36,000 suspicious matter reports, including 140 in relation to the syndicates and individuals referred to in Austrac’s claim,” the bank said.