The 44 dolphins were caught in purse seine nets in three separate events.
The remaining nine dolphins were caught in trawlers.
Dr Stirnemann said the catches were unacceptable.
"For so many dolphins to be caught in one year, in one region, is very alarming."
Dr Stirnemann said the bycatch had been mostly self-reported. She was concerned not all fishers would report their bycatch and "we don't know the full extent of the problem. But even this level of bycatch is unacceptable".
The fishing industry was called to adopt a pledge of zero-bycatch, and to "lift their game".
"This worrying situation also highlights the importance of the planned roll-out of cameras and GPS trackers on boats, so we can see exactly what's going on," Dr Stirnemann said.
In a written statement Dr Jeremy Helson, chief executive of Fisheries Inshore New Zealand, said the recent figures out of the Bay of Plenty region were "very unusual".
"In the previous six years, there were fewer than two captures per year. No fisher ever wants to hurt a dolphin and all skippers do everything they can to avoid that," Helson said
"You will recall in March this year, a Sanford vessel had a mass capture of a pod of common dolphins in one of its nets. The skipper tried to lower the net to release them and, when the dolphins didn't swim out, he released the catch of 30 tonnes of Jack Mackerel in order to save the pod."
Dolphin captures were very rare and the industry did whatever it could to mitigate capture and mortality, but it was never going to be a zero risk environment, he said.
Marine educator Nathan Pettigrew believed purse seine nets were "archaic" and was shocked at the number of dolphins caught.
"Basically I'm not surprised but that amount ... I'm alarmed."
Pettigrew said it was inevitable "with that kind of fishing that something like this would happen".
"I think you kind of need to start looking at what other options there are. It would be good to see some new ways."
Tourism operator Bay Explorer offers daily excursions to watch dolphins and other marine life.
Owner Brandon Stone said the number of dolphins caught was horrific but he was keen to see more science before fishers were potentially unfairly blamed.
Part of this could be the use of cameras on board boats, recording such catches.
What is purse seine fishing?
A purse seine is a large wall of netting deployed around an entire area or school of fish. The seine has floats along the top line with a lead line threaded through rings along the bottom. Once a school of fish is located, a skiff encircles the school with the net. The lead line is then pulled in, "pursing" the net closed on the bottom, preventing fish from escaping by swimming downward. The catch is harvested by either hauling the net aboard or bringing it alongside the vessel.
Source - www.nmfs.noaa.gov
