Bayer's LL Rice 601, engineered to tolerate the herbicide glufosinate ammonium, was discovered in batches of American long grain rice in the EU in August 2006.
At that time the rice variety was not approved for human consumption.
It has since been approved in the US, but no GM rice is allowed in the EU.
Following the incident, which had a large impact on the rice industry, the European Commission introduced emergency measures so that only consignments of US long grain rice that had been tested by an accredited laboratory using a validated testing method and accompanied by a certificated assuring the absence of LL Rice 601 could enter the EU.
It was decided in November 2006 that batches needed to be tested twice because the authorities in the EU and the US could not agree on which testing method was best to ensure a high degree of consistency and accuracy.
According to an advisory issued by the UK's Food Standards Agency (FSA) today, however, agreement has now been reached, removing the need for duplication.
Details on the agreed method were not available prior to publication of this article.
"From now on, each consignment of US rice must be certified free from the unauthorized GM rice, according to the same test method that is used by enforcement agencies in the EU," said the FSA.
The UK government agency said that the amendments to the emergency measures were agreed by the European Members States in December 2007 and came into force at the end of last month.
The European Food Safety Authority has said that the contamination incident was unlikely to cause an imminent safety concern.
However following detection of the GM material, rice futures prices plummeted some $150m. Several multi-million dollar class action lawsuits and individual lawsuits were filed against Bayer by US farmers who suffered severe financial losses.
The USA is one of the major suppliers of rice to the EU.
The EU imports approximately 20.000 tons of long grain husked, semi-milled and wholly-milled rice from the USA per month on average.
The UK's Food Standards Agency has come in for criticism for the way it handled the incident.
A judicial review took place in February 2007, which found in favour of the regulatory agency - but the judge did highlight a number of mistakes made by them in dealing with the emergency.
As a result, the FSA called for the views of stakeholders in advance of a meeting held in London at the end of November 2007.
The FSA would not comment on exactly what was discussed at the meeting, but said a report is being drafted and will be considered by its Emergencies Committee, alongside a draft action plan.