It is the first time the European Medicines Agency has begun a so-called ‘infringement proceeding’ against a drug maker. European regulations lay out numerous requirements for pharmaceuticals, including reporting suspected side effects and submitting such cases to officials.
Nineteen drugs are involved, many of them used for the treatment of cancer, including breast cancer.
The agency did not explicitly state what the side effects were.
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.
If Roche is found to have violated its reporting requirements, it could be fined up to five percent of its sales revenue in the European Union from the preceding year.
The European Commission, the executive body for the 27-country EU, asked the European Medicines Agency to begin 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 said about 80,000 reports by consumers of possible adverse effects to drugs sold in the U.S. had not been properly analyzed. They said there was no evidence that patients were at risk.
In a statement, the European Medicines Agency said 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 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, said the company was working with the EMA to provide more information and it 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 said.
Grotzky said Roche recognized that 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 said.