The fraudsters overcame the Catholic charity's internet security system on 27 November and obtained a number of supporters' names, addresses and credit card details before using them illegally to obtain money. The charity did not know exactly how much its donors had lost.
Although the site experienced a few problems the following Monday, it was not until last Thursday that the gravity of the problem was realised.
The site was shut down, and the police and Charity Commission were informed.
The charity sent emails to more than 2,800 benefactors who had donated online, and letters containing advice and information to its 50,000 contacts.
Neville Kyrke-Smith, UK national director of the charity, said that, because only the most skilled of internet criminals could have penetrated the site, this would narrow the field in the search for the culprits.
However, he added that he feared the hacking would have hit fundraising for crucial aid planned in Pakistan, Iraq and Sudan.
The Charity Commission praised Aid to the Church in Need for its response.
A spokeswoman said that the commission believed it was a one-off incident rather than a wider problem.