Health Minister Isaac Adewole tweeted that tests by the food safety agency found "no evidence" of plastic material.
Lagos customs chief Haruna Mamudu said on Wednesday the fake rice was intended to be sold during the festive season.
Rice is Nigeria's staple food.
Mr Mamudu has not commented on the health minister's statement.
It is not clear where the seized sacks came from but rice made from plastic pellets was found in China last year.
Mr Adewole said the agency would "release detailed findings to public as soon as it concludes investigations", urging Nigerians to remain calm.
Mr Mamudu had said the rice was very sticky after it was boiled and "only God knows what would have happened" if people ate it.
The BBC's Martin Patience in Lagos, who felt the rice, said it looked real but had a faint chemical odour.
The Lagos customs chief had called on "economic saboteurs who see yuletide season as a peak period for their nefarious acts to desist from such illegal" business activity.
Related story: Plastic rice confiscated in Nigeria