On June 15, Tokyo banned sales and imports of Canadian wheat after Ottawa said unauthorised GM wheat plants were found.
"We have decided to lift the ban as we found no such wheat circulated domestically," said an official of the agricultural ministry.
"We will also resume bid tenders next week on condition that all imports should be inspected to check there is no GM wheat mixed in," he told AFP.
Canada is Japan's second largest wheat exporter after the US, accounting for about a third of its total imports for the year to March.
The Canadian Food Inspection Agency said a GM wheat plot was discovered last summer by a farmer in Alberta who was surprised to see wheat resist after a Roundup spray.
Canadian authorities determined the herbicide-tolerant wheat was a banned Monsanto GM wheat line, which had been used in several confined field trials two decades ago in Canada and the United States.
But the world's sixth largest wheat producer said the GM wheat plants were few and posed no food safety risks.
The temporary import bans were another blow to Canadian farmers who faced costly delays in getting grain to markets this year due to a disruption in rail shipping to ports blamed on winter storms.
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