Filipino health authorities said leptospirosis, a bacterial infection, has infected 1,963 people and killed 148 of them.
The outbreak occurred in areas of Manila that remained flooded nearly four weeks after Tropical Storm Ketsana struck the capital on September 26.
A three-member team was flying into Manila "in the next day or so" after the government sought help from the 140-nation Global Outbreak Alert and Response Network to fight the outbreak, Adam Craig, an official of the WHO Western Pacific regional office in Manila, told AFP.
He said the WHO was taking note that it was a "big outbreak and the number of deaths is high," even as the country's medical facilities are "overstretched," partly from heavy damage wrought by the flooding.
"We estimate a five to 10 percent mortality rate," Craig added.
He said the WHO regional office in Manila has also placed orders for rapid diagnostic test kits sought by the Philippines health department.
With 1.28 million residents still living in flooded areas, the Philippines health department estimates 1.7 million people "are at high-risk (of) exposure" to the disease and up to 3,800 could eventually get infected, the WHO said in a report.
The disease, which is transmitted mainly by exposure to contaminated urine of mammals in water in flooded areas, can lead to renal failure.
The Philippines health department earlier ordered 1.3 million people to take antibiotics to protect against disease.
Health Secretary Francisco Duque said Thursday that the outbreak had overwhelmed government hospitals, many of which had also suffered substantial damage from the flooding.
"The sudden upsurge of leptospirosis cases after the massive flooding caused by Tropical Storm (Ketsana) and Typhoon (Parma) brought us to a situation where we need to get into special arrangements with medical facilities from the private sector to help the government treat patients," he said.