In New Zealand chlamydia is not classified as a notifiable disease but is the most commonly reported STI, although the rates have remained stable since 2013.
Unlike syphilis and gonorrhoea, it was more widely reported by females although that was probably due to lower rates of testing in men, ESR public health physician Jill Sherwood said.
It was most common in women aged 15 to 29 with the highest rates among Māori and Pacific Islanders.
Auckland University's School of Population Health reasearch fellow Dr Peter Saxton said that while rising syphilis rate had been a problem for some years, it was a concern to see gonorrhoea rates rise 50 per cent in two years.
It was also the first time there had been data on rates involving men who had sex with men, he said.
Of all the gonorrhoea cases where information was available, 34 per cent were among men who had sex with men despite the fact that group only comprised about 2 per cent of the population, he said.
"That's really alarming. That a third is among gay and bisexual men really is a shock," he said.
"The chickens are coming home to roost after a number of years of lack of strategic direction and underinvestment in sexual health programmes."
Saxton said more funding was needed to make services more available to all groups, in all areas; for education programmes; to hire more sexual health specialists; and to train GPs in how to identify and comprehensively care for the rainbow community in a non-judgmental way.