Rice contaminated with the GMO Bt63 - which is not authorised either in the EU or in China - was identified in rice products imported from China and on sale in EU member states in September 2006.
The Chinese authorities announced measures to address the problem in 2007, including sampling and testing and an official Chinese Inspection and Quarantine Certifical.
Despite this, the presence of some material containing Bt63 was still being reported in some countries late last year.
The Commission's Standing Committee of Food Chain and Animal Health voted this week to introduce the emergency measures as of April 15, for only product consignments that are indicated in a specific Annex of the Decision to enter the EU.
These consignments must be tested by an official or accredited laboratory using a specific testing method.
China, by contrast, has not provided the Commission's Joint Research Centre with control samples it requested, nor with the protocol of the detection method it was using so that the centre could validate it.
The measures will be introduced from April 15 to allow time for practical arrangements to be made.
The situation will be reassessed after six months.
Health commissioner Markos Kyprianou said: "The decision adopted… aims to prevent the unauthorised Bt63 rice from reaching EU consumers, but ensuring that only rice products certified as free from this GMO enter the EU."
He stresses that, under EU safety legislation, only GMOs that have undergone a thorough scientific assessment and authorisation procedure may be placed on the EU market.
The UK Food Standards Agency (FSA), which has said it will soon be providing advice to enforcement agencies, industry and consumers, said it is "not aware of any health implications for consumers who eat rice products containing Bt63".
The FSA has come under considerable fire recently after another illegal GM rice, LLRice 601, unapproved for human consumption, was found in American long grain rice supplies intended for export in August 2006.
Friends of the Earth called for a judicial review, saying the FSA should have done more work with local authorities and the food industry to make sure illegal GM rice was detected and removed from shelves and other parts of the market.
The European Commission has now set out the chain of responsibility for ensuring that imported products do not contain GM material.
It says that China is responsible for ensuring that Bt63 does not enter the EU food chain, and that imports are certified as free from this GMO.
Authorities in member states are responsible for controlling imports at their borders, and preventing contaminated consignments appearing on the market.
Member states should also conduct controls on products already on the market to ensure they are Bt63-free.
Finally, businesses importing rice products from China are responsible for ensuring Bt63 does not enter the food chain, and that imports are Bt63-free.
Under EU food law, business operators are responsible for the safety of food or feed they put on the market.