The World Health Organization (WHO) says a report on North Korea's health system by Amnesty International is unscientific and outdated.
Rights watchdog Amnesty said North Korea was failing to meet its people's most basic healthcare needs.
Amnesty's report is based on interviews with 40 North Korean defectors and foreign health care workers.
In April, the WHO's director visited North Korea and said its health system was the envy of the developing world.
WHO director-general Margaret Chan said the country had "no lack of doctors and nurses".
North Korea has faced critical food shortages and relies on international aid following famine in the 1990s which killed up to one million people.
The country is politically isolated and subject to UN sanctions, which were tightened last year after Pyongyang carried out missile and nuclear tests.
Amnesty's report, The Crumbling State of Health Care in North Korea, was released on Thursday.
It describes barely functioning hospitals, poor hygiene and epidemics made worse by widespread malnutrition.
Many people were also too poor to pay for treatment, the report says. It also cites WHO figures indicating Pyongyang spends less than $1 (£0.65) per person on healthcare a year.
Pyongyang says it provides free healthcare for its people, but witnesses told Amnesty they had had to pay for all services for the past 20 years.
The WHO said Amnesty's report was based on a small sample of people who had left North Korea, some as long ago as 2001.
"All the facts are from people who aren't in the country," WHO spokesman Paul Garwood said in Geneva.
"There's no science in the research."
Mr Garwood said Amnesty's report did not mention recent improvements to North Korea's health care brought about by a programme funded by South Korea and aided by the WHO.
As to Amnesty's claim that people had to pay cash or barter for medical care, Mr Garwood said many field missions in North Korea had not uncovered this practice.
"I'm not saying they're not credible accounts," Mr Garwood said. "But it's not taking into account some of the things that are happening today."
He acknowledged, though, that challenges remained, including poor infrastructure, a lack of equipment, malnutrition and a shortage of medicines.
The BBC's Imogen Foulkes, in the Swiss capital Bern, says a number of UN agencies have aid projects in North Korea and are thought to be reluctant to openly criticise the country for fear of jeopardising their work there.