FlyBe withdrew the Dundee to Amsterdam service in December.
Operating losses at Dundee Airport approached £1m last year, according to new accounts filed at Companies House.
In the year to March 31, the airport recorded a turnover of £2.9 million but had operating costs of £3.5m and administrative expenses of £369,000.
The airport is one of 11 airports operated by Highlands and Islands Airports Limited (HIAL) which is wholly owned by Scottish Ministers and subsidised by the Government.
In the last financial year, HIAL recorded revenues of £22m, an increase of 6.9% from 2016. It recorded a pre-tax loss of £985,000.
Passengers at its 11 airports were 1,658,423, an increase of 15%.
Dundee recorded the greatest increase in passengers out of the HIAL airports as a new route to Amsterdam was introduced last May.
Dundee Airport had 38,700 passengers, compared to 25,576 in 2016.
Flybe withdrew the Amsterdam service in December due to concerns over Dundee’s radar coverage.
HIAL received £20.1m in Government revenue during the year.
