The stalemate highlights continued concern over GMs in Europe, and ministers are not yet won over to allowing them onto the market.
The final approval will now go to the Commission to decide on later this year.
The Agriculture and Fisheries Council met to vote on whether to give the final authorisation for 59122 (Herculex), and the hybrids1507xNK603 and NK603xMON810 to come onto the market.
Previously all three had been given a favourable opinion by the European Food Safety Authority (EFSA) which is in charge of assessing GM products under Regulation (EC) No 1829/2003.
The three products were seeking to be placed on the market to cover all uses except cultivation.
The issue of GM approval within the EU is one of the most contentious in agriculture.
Many Member States, and millions of European consumers, remain steadfastly against the introduction of GM food.
But despite the stringent controls in place, it is becoming harder for Europe's regulatory authorities to deny market access to certain GM products.
The proverbial straw that broke the camel's back was the WTO decision last year that the EU and six member states had broken trade rules by barring entry to GM crops and foods.
The world trade organisation agreed with the United States, Argentina and Canada that an effective moratorium on GMO imports between June 1999 and August 2003 had been put in place.
And although Brussels again began authorising imports of GMOs in May 2004, only seven crops and foods were given the green light.
Further bans were imposed by France, Germany, Austria, Italy, Luxembourg and Greece.
A Commission spokesperson said that for Wednesday's meeting they were unable to " disclose more information as far as the vote is concerned " when asked by FoodNavigator.com.
It is clear that Member States still need to be convinced that introducing genetically modified ingredients into food production is acceptable.
The Commission has asked EU members over ten times to vote on authorising a GM food or feed product, but in the large majority of cases, there was no agreement or simple deadlock.
Luxembourg, Greece and Austria have in the past been some of the more staunch opponents consistently vote against GMO approvals.
The strains discussed yesterday are all said to be insect resistant and herbicide tolerant and were submitted by Pioneer Hibred and Mycogen for 59122 (Herculex) and 1507xNK603 and from US firm Monsanto Company for strain NK603xMON810.
Monsanto won permission last year to import and market three of its genetically modified maize types across the EU for 10 years.
The three products are GA21, a herbicide-resistant maize; MON 863, modified to be resistant to the corn rootworm insect and a hybrid cross between MON 863 and another Monsanto maize strain MON810.
The strains were aimed to resits corn rootworm among other insects, which has earned the nickname the "billion-dollar pest" as the United States Department of Agriculture estimates that this pest causes $1 billion in lost revenue annually to the US corn crop alone.
The Agriculture and Fisheries council meeting was also due to discuss milk, wine and sugar production.