Farm Minister Yoshimasa Hayashi told a news conference that the ban would be lifted on Thursday but with a condition that all incoming US wheat be tested.
The suspension on some imports of US wheat was imposed in May as Japan cancelled a bid for 25,000 tonnes of Western White, a soft white wheat produced in the Pacific Northwest.
Japan imports about 800,000 tonnes of that wheat brand a year, but does not allow genetically-modified wheat.
The Japanese suspension came as South Korea also followed suit while the European Union told its member states to test imports from the area, saying any genetically modified wheat would not be sold to consumers.
The US Agriculture Department initially announced the discovery of the modified wheat. No genetically engineered wheat has been approved in the United States for commercial production. The US department said it was the same breed as a genetically modified herbicide-resistant wheat tested by seed giant Monsanto between 1998 and 2005, but never approved.