The rise of 131,000 new cases was driven by a nine-per cent increase in the Eastern Europe and Central Asia region which accounted for 102,000 new infections - around three-quarters of them in the Russian Federation alone.
In the European Union and Iceland, Liechtenstein and Norway, new infections rose by less than one per cent to 29,000, according to the joint report by the EU agency and the World Health Organisation (WHO).
Among the reasons for the increase is the lack of awareness of anti-retroviral treatments.
"We know that providing anti-retroviral therapy earlier will allow people with HIV to live longer and healthier lives, and will reduce the risk that they transmit HIV to others," WHO regional director for Europe, Zsuzsanna Jakab said.
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AIDS cases were down by 48 per cent in Western Europe between 2006 and 2012, while in Eastern Europe and Central Asia, the number of newly diagnosed cases of the disease caused by HIV increased by 113 per cent.
In 2011 there were 2,300,000 people living with HIV in Europe and Central Asia, according to the WHO.