The move comes after the European Commission asked the regulator to investigate reports from authorities in Finland and Sweden of a small number of cases where children developed a rare sleep disorder after receiving Pandemrix.
Finland has suspended the vaccination of children and adolescents until the probe is complete.
Pandemrix was approved by the EMA in September 2009 during the H1N1 flu pandemic and has been given to at least 30.8 million Europeans.
Narcolepsy causes sufferers to fall asleep suddenly and unexpectedly. Its precise cause is unknown, but it is believed to be triggered by a combination of genetic and environmental factors, including infections.
The EMA said its Committee for Medicinal Products for Human Use (CHMP), the influential expert group which originally approved the vaccine under a fast-track procedure, will look closely at all available evidence.
While narcolepsy was reported after vaccination in a number of children, the regulator will probe whether there is a genuine causal link between the illness and the vaccine.
Experts are expected to consider the 'background rate' for narcolepsy – the normal number of cases seen in a large population of young people – to figure out whether the connection is merely a coincidence.
Experts from across the EU will be drafted in to help assess the safety concerns. If a link with narcolepsy is found, it may lead the EMA to review its advice on the risk-benefit balance of Pandemrix.
The agency is also working with the World Health Organisation (WHO) and the European Centre for Disease Prevention and Control (ECDC).
The news comes as a blow to GSK, makers of Pandemrix, which has benefited from multi-million euro contracts with European governments.
However, companies manufacturing H1N1 vaccines are not liable for unforeseen side-effects of the products thanks to immunity clauses included in contracts with governments that bought the vaccine during the pandemic.
On 10 August 2010, the WHO declared that the H1N1 outbreak had entered the 'post-pandemic phase'.
