A conman nabbed the cash after convincing call centre staff to issue a credit card in Mr Agius' name.
Along with personal details about the well-known executive, the fraudster was able to simply walk into a branch of Barclays and withdraw the money with the card.
Barclays said that it has begun a review of data security and said that Mr Agius has been paid back by the bank.
"All Barclays customers, from the chairman downwards, have a 100 per cent fraud guarantee as long as they take responsible care of their information," a bank spokesman said in the Times.
Identity fraud is believed to cost banks more than $3 billion every year, with over 40,000 scams committed annually.
Mr Agius commented: "Credit card fraud is an issue which our industry continues to confront. Barclays is resolved to do everything possible on behalf of our customers, to minimise its impact."
The chairman took on the job at Barclays last January and receives an annual salary of Â£800,000 plus bonuses.