He died after a short illness, the organization said.

Besides his efforts to fight infectious diseases, including AIDS, tuberculosis and dengue fever, Dr. Nakajima enlarged the organization's focus on preventive medicine and vaccinations for children, and tried to rally international support to end ritual female genital mutilation. In a statement on Monday, Dr. Margaret Chan, the current W.H.O. director general, praised his efforts to defeat polio.

But he came under frequent criticism. The United States and other Western nations twice opposed his election as director general of the agency, which is part of the United Nations. They argued that he had not infused the agency with a clear sense of direction and had let its budget and bureaucracy balloon.

In 1992, when Washington was fighting Dr. Nakajima's re-election, Louis W. Sullivan, the secretary of health and human services, wrote, "It appears that W.H.O. is losing its reputation as the world's leader in health matters at a time when serious global health problems present daunting challenges to us all."

Dr. Nakajima was again cast in a harsh light when Dr. Jonathan Mann, the widely respected commander of the United Nations's fight against AIDS, resigned in 1990. In an interview with The New York Times, Dr. Mann said he resigned over "issues of principle" and "major disagreements" with Dr. Nakajima, who wanted to de-emphasize AIDS prevention and put more effort into other diseases, like malaria.

Dr. June Osborn, chairwoman of the National Commission on AIDS, called the resignation of Dr. Mann, who died in 1998, "a world tragedy."

In the 1992 director general election, the United States accused Japan of overly aggressive tactics in promoting Dr. Nakajima's candidacy. The State Department said Japan had threatened to cut off fish imports from the Maldives and coffee imports from Jamaica if those countries did not support Dr. Nakajima. A spokesman for Japan's Foreign Ministry denied the accusations.

There were also allegations that Japan had awarded research contracts to 23 of the 31 W.H.O executive board members who recommended Dr. Nakajima's re-election. A W.H.O. audit found that the contracts — the largest of which was $150,000 — were technically legal but presented "a problem of ethics," in the words of the board chairman, Jean-François Girard of France.

Dr. Nakajima defeated Dr. Mohammed Abdelmoumene of Algeria, who had been his deputy, in a 93-58 vote. It was the first time in the organization's history that an incumbent director had been challenged by another W.H.O. official.

In 1997, Dr. Nakajima announced that he would not seek a third term, in part because he had lost support from African nations after he had explained the relative scarcity of Africans in executive positions at the agency by suggesting that Africans had difficulty conceptualizing and writing reports.

The Economist magazine said the remark "was particularly odd coming from Dr. Nakajima, who has himself been accused of quasi-incomprehensibility, even when he speaks Japanese."

Dr. Nakajima was born in Chiba-shi, Japan, on May 16, 1928. He graduated from Tokyo Medical University in 1955, representing the 10th generation of his family to produce a doctor. After studying psychiatry and pharmacology at the University of Paris, he returned to Tokyo Medical University to earn a Ph.D. in medical sciences. He then became research director for Nippon Roche, the Japanese subsidiary of Hoffmann-LaRoche.

Dr. Nakajima joined the W.H.O. in 1974, and worked to improve getting medical supplies to the third world. He helped develop the concept of "essential medicines," drugs that satisfy the health care needs of most of a population. In 1979, the Western Pacific nations elected him regional director, and he served two terms.

Dr. Nakajima is survived by his wife, the former Martha Ann DeWitt, and two sons.