Nakajima, who led the Geneva-based WHO from 1988 to 1998, died in Poitiers in western France on Saturday after a short illness, the agency said in a statement.
His decade-long term at the head of the WHO was a controversial one, marked by accusations of financial mismanagement and dubious priorities.
It also involved a famous conflict with the former director of the WHO's anti-AIDS programme, Jonathan Mann, who resigned in protest in 1990.
Mann told the New York Times after his resignation: "We're facing a very important worldwide epidemic that requires continual innovation and action, and Dr Nakajima and I do not see eye to eye on the importance and strategy of the fight against AIDS."
The WHO stressed Monday that Nakajima had been the driving force behind some of its most successful programmes, including its strategy for treating and reining in tuberculosis and the expansion of its global vaccination programme for children.
"For all of these initiatives, the impact on people's health mattered most to him," current WHO chief Margaret Chan told a meeting of the organization's executive board in Geneva, according to the statement.
"One of Dr Nakajima's greatest passions was to see polio defeated," Chan said.
"We are doing so now . . . let these efforts also be a tribute to his memory," she said.
The participants at the Geneva board meeting honoured Nakajima, who is survived by his wife Martha Nakajima and two sons, with a minute of silence.