Singapore Airlines will temporarily reduce the number of flights from Canberra to Singapore and Wellington for three months from August.
Instead of flying four times a week there will be three flights in one week of August, September and October, resulting in a net loss of three services overall.
Spokesman Karl Schubert said the decision was part of normal operations.
"During low season we regularly make ad hoc changes to our flight schedules to meet market demand and ensure we are optimising the performance of the route during low season," Mr Schubert said.
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"We will work with affected customers to re-accommodate their travel requirements."
Singapore Airlines introduced the "capital express" service in September last year with four flights a week.
The cancelled flights from Canberra to Singapore were scheduled for Monday, August 14 and Tuesday, September 5 and October 24.
Canberra resident Helen Gladman told Fairfax Media she was notified this week that her Canberra-Wellington flight in September to attend a wedding had been cancelled.
"I got a text yesterday from the airline advising the flight was cancelled and my husband and I were moved to a flight two days later. This wouldn't work," she said.
"Thankfully we had booked through an agent who contacted the airline for us.
"We were offered a full refund or two other flights, thankfully on the same day we originally planned, which were via Melbourne or Sydney.
"Not ideal but at least on the day we wanted in the first place."
Singapore Airlines is currently reviewing its flights to and from Canberra.
In January, Canberra Airport's head of aviation Matthew Brown said federal government figures showed load rates (the number of passengers per flight) averaged 83 per cent capacity for the Canberra-Singapore flight.
"Based on these figures, the viability of the route shows that it is well established and becoming more popular," Mr Brown said.
"We are in constant dialogue with Singapore Airlines and are pushing for the addition of the fifth service in the near future, but understand that this will be a commercial decision by the airline."
The ACT Government has been active in attracting international carriers to Canberra.
Chief Minister Andrew Barr visited Singapore last month and met with Singapore Airlines.
Mr Barr said visitors from Singapore increased by 73.5 per cent in 2016 after regular flights began.
"The ACT Government is looking to encourage more two-way visitation," he said.
"During this trip, I have met with Singapore Airlines to discuss the success of these flights up to this point and the possibility of increasing the number of flights out of Canberra."
It's understood travel agents were advised of the cancelled flights this week.
Singapore Airlines is expected to resume four services every week in November.