Erroneous settings on water gauges lowered groundwater levels at half of the dozen nearby wells to three feet below the required safety levels.
When groundwater at one well briefly sank below the level of the contaminated water in May, it might have caused radioactive water to leak into the soil.
Tokyo Electric Power (Tepco) is the firm responsible for Fukushima.
Tepco spokesman Shinichi Nakakuki said that their samples did not show an abnormal increase in radioactivity and leaks to the outside are unlikely.
Risks of a leak were unlikely because groundwater levels at wells dug closer to the reactors have stayed above minimum safety levels, said Mr Nakakakuki.
Tepco is investigating the potential contamination after it discovered the problem this week.
The Fukushima plant was crippled by a massive undersea earthquake which sent a huge tsunami sweeping across Japan's northeast coast on 11 March 2011.
Cooling water has been leaking from the plant's damaged reactors and mixing with groundwater pooling in the basements of the reactor building, increasing the total amount of contaminated water.
The wells around the reactor are designed to pump groundwater away from the basements and reduce the amount around the reactor area.
More than 18,000 people were killed in the disaster, and the damage to the Fukushima plant was the worst of its kind since the Chernobyl nuclear disaster in 1986.
Three of Fukushima's reactors went into meltdown, and locating the fuel debris caused by that has been a key part of the Japanese government's decommissioning process for the plant.
In July, an underwater robot spotted lava-like rocks which are believed to be missing melted nuclear fuel from Fukushima.
Last year, the Japanese government said it expects the total costs including compensation, decommissioning and decontamination to reach £150bn.
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