The airline was offering flights from Lisbon to Hong Kong – via London – for just $1,512 (£1,179), according to the South China Morning Post.
The journey usually costs around $16,000 (£12,469).
It is the second fare blunder this month for the Hong Kong-based airline, but the company said it would honour the price.
“We are aware of an error on some fares from Europe on our website because of an input issue,” a spokesperson told Sky News:
“The sale of such fares was stopped immediately.
“We are looking into the root cause of this incident both internally and externally with our vendors.
“For a very small number of customers who have purchased these tickets, we look forward to welcoming you on board to enjoy our premium tickets.”
In its New Year’s Eve travel sale, some eagle-eyed customers noticed Cathay was offering first-class and business-class tickets from Vietnam to New York at a huge discount.
Customers paid $675 (£529) for a return flight in August that usually costs $16,000 (£12,541).
It turned out to be an error, but the airline again promised to honour the price.
It comes at a difficult time for Cathy Pacific, which is trying to turn around its fortunes as it faces stiff competition from low-cost Chinese airlines.
Last March, it posted a loss of £115m for the year to December.
And more than nine million Cathy customers had their personal information stolen when its computers were hacked last year.