The storm was downgraded from a typhoon after sweeping past Tokyo earlier Friday, where it failed to disrupt the morning rush-hour, but was still packing winds of up 83 kilometres an hour and bringing heavy rain.
Workers at Fukushima had been scrambling to insulate the plant from any storm damage, but Neoguri appeared to have little impact on the site as it headed out into the Pacific.
"We are not seeing any rainfall or strong winds" near the plant, a local weather agency official said. "The impact of the storm is likely to fade out soon," he added.
Japan's weather agency had issued strong wind and rain warnings for the Fukushima region but later said the weather was forecast to improve Friday afternoon.
A spokesman for the plant operator Tokyo Electric Power earlier said the situation was stable.
"We are conducting today's operations as scheduled while monitoring any impact from the typhoon," he said.
Neoguri, which hit the mainland Thursday morning, reached Futtsu in Chiba prefecture, some 45 kilometres southeast of central Tokyo, shortly before 5am (3am Thailand time), the Japan Meteorological Agency said.
Television footage showed high waves slamming into breakwaters in Chiba, while emergency officials hurriedly built temporary barriers against further landslides.
But the impact of the typhoon on the capital was limited, with train and flight services running as normal during the morning rush hour, local media reported.
More than 680 houses in several prefectures were earlier flooded or damaged due to the typhoon and heavy rain, according to the disaster management agency, with about 489,000 households urged to seek shelter.
Officials said there was still a risk of flooding and landslides from Neoguri, which earlier in the week prompted local authorities to urge half a million people to seek shelter in Okinawa.
More than 60 people were left injured by the storm, officials and reports said, while as many as seven deaths have been directly or indirectly linked to the typhoon.