The association said it had been in negotiations with all of New Zealand's District Health Boards (DHB) since December 2015 for a new collective agreement that covers resident doctors.
Resident doctors across the country have been working rosters, including seven nights in a row and 12 days in a row. The association believed this roster was unsafe for patients and unsafe for the doctors.
It is thought that thousands of patients nationwide would be affected by the strike .
Julie Patterson, lead CEO for the DHBs' Employment Relations Programme and Whanganui DHB CEO, said the Bay of Plenty DHB had postponed 350 planned surgeries and appointments.
This strike, following a similar two-day strike last October, was hollow and futile considering the DHBs met the union's pay and roster demands in their original claim last year, she said.
"The strike will not influence the combined DHBs' position," Ms Patterson said.
"This situation will be reflected right around the country causing unnecessary discomfort and inconvenience to many thousands of patients in need of treatment."
In talks with the union, the DHBs have agreed to reduce rosters of 12 days in a row, which were considered a risk to patients and the doctors who worked them, to a maximum of 10.
This results in more days off.
NZ Resident Doctors' Association national secretary, Deborah Powell said: "There is a reduction in pay associated with us not working the hours."
NZME understands the proposal would lead to doctors not claiming pay for around one- third of the days off.
However, the union also wants members to be able to take the days off around weekends and the DHBs have not agreed to this, arguing it would leave them with too few resident doctors at key times, especially on Mondays and Fridays, and too many on Wednesdays.
_ Additional reporting, NZME
The facts in the Bay of Plenty:
Total resident doctors employed: 162
Total resident doctors working on affected rosters : 93
There are seven rosters affected in the Bay of Plenty.
Two rosters have not been fixed at all.
Five rosters have been partially fixed.
Number of resident doctors required for safer rosters: 6.4