Japan's capital of Tokyo is now on high alert in anticipation of Typhoon Neoguri which is expected to reach areas near the tsunami-crippled Fukushima nuclear power plant on Friday.

The company said workers have been tying up cables and hoses, as well as cranes and booms so they won't fall. A company spokesman likewise said employees have been stationed in areas to monitor possible water flow coming into the plant, which could further enlarge the quantities of already contaminated water in the facility.

On Thursday, Typhoon Neoguri, downgraded from a typhoon to a "severe storm," struck the Japanese mainland. It triggered massive flooding, toppled down trees and engulfed houses in mud.

Public broadcaster NHK reported over 680 houses in several prefectures were flooded due to the typhoon's heavy rains. Some 489,000 households have been urged to seek shelter.

Read: Typhoon Neoguri: 2 Dead, Forces Flights Cancellation, Cuts Electricity and Water Supplies (PHOTOS)

"Water kept gushing into the house no matter how hard we tried to pour it out. We kept shoving out water all night," a woman in northern Yamagata Prefecture told AFP.

Five people have died in the wake of the storm. The number of injured were recorded at over 60 people.

Read: Super Typhoon Neoguri Update: Okinawans Urged to Relocate; Expect Massive Wind Damages, Flooding; JMA Raises Highest Alert; Kadena Air Force Base at Risk

Neoguri is expected to move northeast over the Pacific coastline before gradually leaving the Japanese archipelago, the Japan Meteorological Agency said.

The storm's wind gusts is still currently up to 126 kilometres per hour.

Read: Japan Advised to Brace for Neoguri, 2014's First Super Typhoon; Okinawa Will Receive Worst Impact