Applicants queue up to apply for US visas under the rain outside the US Embassy in Manila as the tailend of Typhoon Kalmaegi continues to dump rain across the northern part of the Philippines on Monday.

AFP

Typhoon Kalmaegi swept out of the Philippines on Monday after causing chest-deep floods in some rural areas but largely leaving the storm-prone country unscathed, authorities said.

The storm, with winds of 160 kilometres an hour, struck the northeast of the main Philippine island of Luzon on Sunday evening, then moved west across land before heading into the South China Sea on Monday.

Three people were killed and three others remain missing after a passenger ferry sank in the central Philippines on Saturday evening amid rough weather as the storm approached.

But officials said this was not directly linked to the typhoon, and said there had been no reports of other casualties related to the weather.

"We have no casualties... because we gave out advance warnings, because our local chief executives acted early, because we had pre-emptive evacuation and took our countrymen out of danger," Interior Secretary Manuel Roxas said.

But he also described the storm as only "moderate", and it did not hit heavily populated areas extremely hard. Floods occurred mostly in the mountainous and farming northern regions of Luzon.  

About 7,800 people sheltered from the typhoon in government evacuation centres, but Roxas said many of them were returning home soon after the storm passed.

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