The first flight from Whangarei to Auckland was at 7am.
From November 1, the number of flights each way remained the same but departure times changed.
Flights from Auckland depart at 6.05am, 10.05am, 3.45pm, and 7.30pm Monday to Friday and on Sunday.
Whangarei to Auckland departure times are 7.10am, 11.10am, 4.10pm and 7.55pm.
The new schedule means medical professionals leaving Auckland for Whangarei at 10.05am can only squeeze in three to four hours of work before returning on the 4.10pm flight.
An Air New Zealand spokeswoman has said issues with delays to the last flight from Whangarei on a Friday have historically occurred as a flow-on effect of the inbound aircraft waiting in Auckland for customers connecting from other services.
"In building the new schedule, we did our best to take in to account the preferences of in-bound and out-bound, and we consulted with local leaders when determining the schedule."
Dr Chamberlain said NDHBw as one of the biggest employers in Northland and a major user of Air New Zealand services.
He said locums and medical professionals travelled to and from Whangarei almost daily to provide patient clinics across Northland.
Medical specialists travelled to Northland to provide paediatric surgery and cardiology, dermatology, rheumatology and hepatology treatment. Paediatric specialists have between two and four clinics a month in Whangarei, attended by between 10 and 13 patients a clinic.
"Due to the recent changes in the flight times these medical professionals now have to fly the night prior to the clinic, stay a night in Whangarei and then attend the clinic the following day.
"This has caused added financial burden to our DHB and often takes the medical professional away from other duties.
"This is also causing pressure on our clinics due to the restricted times they can occur to allow the travelling clinicians to make the flight times.
"As a result, patients may have to wait longer for their health services or be required to travel to Auckland for their health services," Dr Chamberlain said.
Costs incurred in billeting health professionals overnight could be well spent in other areas, he said.