Papua New Guinea's prolonged cholera outbreak has surfaced in the capital Port Moresby, claiming three more lives and raising fears it could spark a major epidemic.

The three men who died last week all lived in Port Moresby's coastal village communities, Hanuabada and Lealea.

PNG's Post Courier newspaper reported 11 others have been diagnosed with the intestinal infection, that is mainly transmitted through contaminated water and food and is closely linked to inadequate environmental management.

A PNG health department circular obtained by AAP confirmed cholera is present in Port Moresby.

"We have confirmed the diagnosis by laboratory support from Central Public Health Lab for a couple of the cases.

"This disease has the potential to cause a major epidemic in the city and its peripheries if appropriate control and preventive measures are not seriously taken into consideration," it stated.

Estimates are that since the first cholera case was reported in August 2009 more than 3000 cases have been confirmed nationwide with estimates of between 60 and 100 related deaths.

A public health emergency was announced in September last year after a series of cholera outbreaks were diagnosed across the country but poor planning and lack of government agency coordination has fuelled continued outbreaks.

NGOs, church groups and aid agencies are assisting the PNG government to tackle the nationwide problem.

This is PNG's first cholera outbreak since the 1960s.

- AAP