The man drowned in a river in the city of Tuguegarao on Monday morning as Megi approached the area, Benito Ramos, the nation's civil-defence chief, said.
The northeastern provinces of Cagayan, in which Tuguegarao is situated, and Isabela were the first to feel the impact of the typhoon.
Megi, dubbed a "super-typhoon" by government relief agencies, has brought winds with speeds of up to 260kph, the government weather station said.
The storm was not expected to hit Manila, the capital, directly but authorities have warned the city's 12 million residents to remain on alert.
Schools were closed and thousands of people were evacuated across the north of the Philippines' main island of Luzon in advance of the storm, rescue and relief officials said.
Megi is expected to exit out to the South China Sea on Tuesday.
Benigno Aquino, the Philippines' president, has ordered all government agencies to be on high alert to prevent casualties, while the coast guard was instructed to ban all fishing vessels from setting off to sea in the north.
"The president is reiterating that all agencies concerned should be ready for the approaching super typhoon Juan [Megi]," Abigail Valte, a deputy spokeswoman for Aquino, said.
She cautioned the public against complacency, amid reports that the weather in some northern provinces remained clear as of early Sunday.
Norma Talosig, the regional chief of the civil defence office, said the government was not ruling out forced evacuation for those who refused to leave their homes despite being told to do so.
"Our main objective is the safety of the community, the safety of the responders."
In Manila, disaster officials said food packs, medicine and rescue equipment, including rubber boats, were ready in areas expected to be lashed by the typhoon.
The Philippines is battered by an average of 20 typhoons a year, some of them deadly.
Tropical Storm Ketsana and Typhoon Parma struck the northern Philippine island of Luzon within a week of each other in September and October last year, triggering the worst flooding in recent history.
The twin storms killed more than 1,000 people, affected nearly 10 million and caused damage to $4.3bn of infrastructure and property, according to the World Bank and international humanitarian agencies.
The US navy's Joint Typhoon Warning Centre in its latest advisory on Sunday said Megi had undergone "rapid intensification", but could weaken as it moves across mountainous terrain after hitting Luzon.
Megi would then begin to steadily reintensify as it leaves the country heading for the South China Sea, it said.
China has urged its vessels to take shelter in ports and urged local authorities to prepare for emergencies caused by wind and rain, Xinhua said.