Tropical Storm Shanshan slowly made its way northeast through Japan toward the capital Saturday, setting off a mudslide that killed three people, halting trains and leaving underground passages brimming with water.

Meteorological officials warned of torrential rains they compared to a waterfall in major cities like Osaka and Tokyo.

The storm, packing winds of up to 65 kilometers (40 miles) per hour, crawled over the southwestern island of Shikoku and the main Honshu island at a speed of 10 kph (6 mph), forecast to affect parts of Japan through Sunday and Monday, although its exact route was uncertain, the Japan Meteorological Agency said.

At least six deaths were believed to be related to the storm, according to public broadcaster NHK, including a person who was swept by a river, another crushed by a fallen roof, and a man slammed onto the road by a blast of wind in southwestern Japan, as well as the three killed in the mudslide.

A man who went out on a boat was missing and 125 people were injured, according to NHK, which compiled tallies from local governments.

Damage from the heavy rainfall hit a wide area, including more than 1,000 kilometers (600 miles) away from the center of the storm. News footage showed overflooded rivers and cars immersed in muddied waters in Kanagawa Prefecture, southwest of Tokyo, when the storm was technically still in southwestern Kyushu.

The meteorological agency issued heavy rainfall and mudslide warnings to Aomori, in northeastern Japan, for Saturday evening. The local government of Suginami ward in Tokyo warned residents in risk areas to be ready to evacuate in case of mudslides.

Dozens of flights were canceled and airlines scheduled alternate flights for stranded passengers. In southwestern Japan, the storm left a broken bridge, as well as layers of mud and branches strewn on roads.

Initially categorized a typhoon, the storm made landfall Thursday. It has since weakened, but its slow movement means intense rainfall lasts for long periods in a relatively large area.