The German company admitted the mistake to investigators in Brussels after the discovery of the seeds in a field in south central Sweden.
The German company, which is authorised to grow a strain called Amflora but not the new, experimental Amadea variety, told the European Commission that the wrong seed was fed into the wrong tube, according to commission spokesman Frederic Vincent.
Vincent said that while Brussels "took note" of the explanation, it wanted answers on quality control checks at laboratory level in Germany as well as in the fields where Amflora is grown in the Czech Republic, Germany and Sweden.
Commission officials will travel next week to "clarify the magnitude of the contamination in all seed lots of Amflora," Vincent added.
An expert at environmental campaigners Greenpeace, which initially brought the contamination to light, said BASF's explanation was "worrying."
Marco Contiero said the company "has not answered if other countries also have this problem," and urged that all Amflora sites "starting with Sweden" be destroyed as a precautionary point of principle.
Regional authorities in northen Germany already on Tuesday banned Amflora for these reasons.
Brussels "strongly stressed that since Amadea is not authorised, it will not accept its growing in EU fields other than experimental fields," Vincent underlined.
Amflora is a strain of potato that is authorised for the likes of glue or paper-making, but not human consumption.
Greenpeace claims that Amadea, the subject of an application for authorisation just days before the seeds were found in Sweden, has been "grown illegally in open fields in Sweden for months."