[1] Xangsane made landfall in the Philippines, battering the northern islands with torrential rains and strong winds, and causing widespread flooding and landslides.

After passing over Manila and emerging over the South China Sea, the typhoon made a second landfall in central Vietnam, also causing flooding and landslides there and in Thailand.

[6] Simultaneously, the Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA) began releasing warnings in relation to the tropical depression with the local name Milenyo.

[7] The system quickly organized as it drifted westward, and according to both the JMA and the JTWC, it attained tropical storm intensity near 00:00 UTC on September 26.

Over the next several hours, Xangsane rapidly intensified as it approached the archipelago;[5] the JMA estimates that the typhoon achieved its maximum 10-minute sustained winds of 155 km/h (96 mph) early on September 27, with a corresponding central pressure of 940 millibars (28 inHg).

[6] With a well-defined eye evident on visible satellite imagery,[8] Xangsane struck southern Luzon around 12:00 UTC, and remained over the Philippines for the next day or so.

[5][6] Due to extensive interaction with land, the typhoon's structure deteriorated, and the JMA downgraded it to a severe tropical storm early on September 28.

[5][9] Over open waters, the system encountered conditions favorable for renewed intensification, including warm sea surface temperatures, light vertical wind shear, and strong upper-level divergence.

[7] Tracking westward at around 17 km/h (11 mph),[10] Xangsane maintained its intensity until it neared Vietnam, when dry air and land interaction began to slowly diminish the typhoon on September 30.

[14] Prior to Xangsane's final landfall, the Vietnamese government set up a steering committee headed by Deputy Prime Minister Nguyễn Sinh Hùng to oversee evacuations and storm preparations throughout central Vietnam.

[21] Rough waters and seaport closures left at least 3,400 people and nearly 270 vehicles stranded in ports and terminals, mainly at the primary ferry crossing between Samar Island and Bicol Region.

[20] The local and regional Philippine National Red Cross chapters reported major damage in at least 116 municipalities, 12 cities, and a total of 1,295 barangays across the country.

[27] The remnants of Xangsane moved over Thailand on October 2 and combined with monsoonal moisture over the north central part of the country, causing torrential rains and severe flooding in over 35 provinces.

Senator Miriam Defensor Santiago wrote an appeal to President Gloria Macapagal Arroyo, asking her to approve the "Anti-Billboard Blight Act of 2006", which would ban billboard advertising on major thoroughfares within Metro Manila.

On October 13, a minivan carrying a relief team from a local government in Ho Chi Minh city was caught in an accident, killing 12 aid workers.

[34] The Department of Disaster Prevention and Mitigation and the Thai Red Cross Society evacuated residents from areas of central Thailand that had been affected by flooding from the remnants of Xangsane.

[28] As a result of the deaths and damage caused, it was decided at the 39th annual meeting of the ESCAP/WMO Typhoon Committee in Manila in December 2006 that the name Xangsane, along with four others, would be retired from the name list.