It is the first time the agency has begun such proceedings against a drug maker. European regulations lay out numerous requirements for pharmaceuticals, including reporting of suspected side effects and submitting such cases to officials.
If Roche is found to have violated its reporting requirements, it could be fined up to five percent of its turnover in the European Union from the preceding year.
Nineteen drugs are involved in the EU infringement procedure, including many for the treatment of cancer. There were more than 15,000 deaths among the reports of possible side effects, though it was unclear if those deaths were linked to Roche medicines.
The European Commission, the executive body of the 27-country EU, asked the European Medicines Agency to instigate the infringement process.
British authorities brought the problem to the attention of the European authorities in May after noticing "serious shortcomings" in how Roche AG reported potential side effects. Regulators say about 80,000 reports by consumers of possible adverse effects to drugs sold in the U.S. had not been properly analyzed. They says there was no evidence patients were at risk.
In a statement, the European Medicines Agency says it will further investigate the allegations against Roche.
"We issued Roche with a detailed letter setting out the allegations against them and they now need to respond," said Martin Harvey Allchurch, a spokesman for the European Medicines Agency. He said the agency had 18 months to finish its investigation. It will then be up to the European Commission to decide whether Roche should be penalized.
Daniel Grotzky, a Roche spokesman, says the company was working with the EMA to provide more information and that they did not want to speculate on the outcome of the investigation. "Both the EMA and other health authorities have consistently said there is no change to the safety profile of our drugs," he says.
Grotzky says Roche recognized some adverse events had not properly been reported in the past. "We are taking measures within the company... to make sure this does not happen again," he says.