The cyberattack has impacted the company's Nook services, an ebook reader and storage platform which was launched in 2009.
The information that the intruders may have got access to include names, addresses, personal information and purchase histories, the company said, according to a report in The Register on Thursday.
A number of Barnes & Noble customers took to social media over the weekend to complain about outages, according to a report in Bleeping Computer.
While some said that they could not access their Nook libraries and the books they had earlier bought, others found difficulty in logging in to the company's online platform.
"We are continuing to experience a systems failure that is interrupting NOOK content. We are working urgently to get all NOOK services back to full operation. Unfortunately it has taken longer than anticipated, and we sincerely apologize for this inconvenience and frustration," the official Barnes & Noble Customer Service Twitter handle said on Wednesday.
"Please be assured that there is no compromise of customer payment details which are encrypted and tokenized. We expect NOOK to be fully operational shortly and will post an update once systems are restored," it added.