Environmental campaign group Greenpeace is now calling on the company to issue a list of other firms that are buying the sweetener developed by Meiji for use in their products.
The GF2 sweetener is described as a sugar alternative and targeted at the weight loss foods market.
The company had not filed the appropriate paperwork to gain approval for the ingredient in Japan however, said a Greenpeace GMO campaigner, Sachiyo Tanahashi.
"The consumer doesn't even know if it is safe," she told ConfectioneryNews.com.
"Meiji has also told us previously that they have a GMO-free policy." Meiji Seika could not be reached by ConfectioneryNews.com but a spokesman at the firm told Reuters that "we're confident about the safety of the products based on a pile of test data we've collected".
The company plans to apply for approval from the health ministry "as soon as possible" so that it can return to selling the sweetener, he said.
Meiji issued a voluntary recall on Wednesday last week of sixteen products containing the sweetener including chocolate, cocoa and a snack bar as well as the sweetener sold as a stand alone product.
Another food firm, Fuji Food, has also recalled several products containing the sweetener.
But Greenpeace says other products containing GF2 may remain on the market.
Sweeteners are seeing booming demand around the world as consumers seek to avoid sugar for weight loss reasons.
Recent research by Mintel found that just over 34 per cent of UK consumers are now actively avoiding sugar, while in France and Germany, the figures are 40 per cent and 37 per cent respectively.
Selling sweeteners made with GM ingredients is a different story however.
Japan has approved 36 different varieties of GM corn for human consumption as well as other food ingredients.
But Greenpeace claims labeling laws are weak and confusing to consumers.
Under Japanese food labeling laws, only the top three ingredients by weight in a food product are required to be labeled if they are genetically modified, and then, only if they are above a 5 per cent threshold.
Highly processed products such as soy oil are not required to be labeled.
"We're also asking the government to improve labeling laws," said Tanahashi.
"The consumer doesn't know when they're eating GMO food."
Japanese consumers show considerable resistance to genetically modified food products when surveyed but researchers say that better marketing and information could improve uptake.
Research by a team from Canada published in the Journal of Food Products Marketing in August 2006 concluded that safety and specific quality benefits of GM food need to be effectively communicated to Japanese consumers through reliable sources and media if marketers wish to increase willingness to accept GM food.