Roche is under scrutiny by European regulators for allegedly failing to follow procedures regarding the reporting of side effects associated with its medicines under the EU's pharmacovigilance legislation.
The investigation is the first of its kind in Europe and - if found guilty - Roche could face a fine of up to 5 per cent of its annual turnover, which was 12.8bn Swiss francs ($13.7bn) last year.
The EMA launched the probe at the request of the European Commission and follows a damning report of Roche's pharmacovigilance operations earlier this year by the UK Medicines and Healthcare products Regulatory Agency (MHRA).
The regulator found "serious shortcomings" in Roche's processes, according to an EMA statement, although the agency stressed there is no suggestion at the moment that the benefit-risk profile of the pharma company's products has changed.
The investigation centres on 19 Roche products that were approved under the EU's centralised authorisation system and has been brought under Article 5 of Commission Regulation (EC) No 658, which came into effect in 2007.
According to a Reuters report, the investigation is running alongside another probe into the public health implications of Roche's alleged lapses, which relate to a failure to assess up to 80,000 cases of possible adverse drug reactions.
The adverse event reports were from an access programme run in the US for patients who were unable to afford the medicines, and had not been reported to the EMA, said the news agency.
The EU has just undergone a major revamp of its pharmacovigilance legislation, with a new Regulation and Directive adopted in July that bring in a raft of new compliance obligations for pharma companies.
Among the measures introduced is the pharmacovigilance system master file (PSMF), a document detailing the global availability of safety information for medicinal products, and other requirements designed to boost pharma company transparency. Member states have until the end of 2013 to implement the changes.