It meant that revenue for April was just $105,000, down from $649,000 on the year prior.
Passenger numbers for the entire year were 541,000, down 28 per cent to levels seen in 2015 before Jetstar entered (then left) the Hawke's Bay market.
HBAL board chairwoman Wendie Harvey told the council the loss will "certainly come as no surprise" and there were three main factors impacting the result.
Covid-19 was a factor alongside "really significantly" Jetstar exiting the airport in December 2019 and impact of Covid-19 striking in the middle of the terminal rebuild.
The loss also included the write off for the old terminal of $1.371m.
"Although the result is disappointing the fact that we are here and well on our way to recovery is down to the sheer commitment and resilience of people we have.
"In short it was probably the most challenging experience that a number of us have been through in our working life."
She also spoke of the impact another Covid-19 lockdown situation could have.
HBAL chief executive Stuart Ainslie said it would have about a half a million dollar impact a month on businesses.
Since the financial year end, Harvey said the airport was "tracking well in terms of recovery".
Councillor Simon Nixon said it was a "result better than one could anticipate" and interim numbers for the second half of the year suggested there had been "quite an astonishing recovery".