Participants in the EU Emissions Trading Scheme based in Ireland reported 5.4% more greenhouse gas emissions in 2016 than in 2015.
This is compared to a decline of approximately 2.7% across Europe in Emissions Trading Scheme emissions.
Emissions from Irish power generation sector were up by 6.6% with an increase of 6.8% from the cement sector and 5.1% from food and drink sector respectively.
In the aviation sector emissions growth was 23% - although this was mainly due to increased traffic there were also some changes in the attribution of flights to Ireland previously reported to another country in the scheme.
In Ireland, 100 major industrial and institutional sites in Ireland participate in the Emissions Trading Scheme.
These include sites operating in the power generation, cement, lime, and oil refining sectors.
Also included are large companies in sectors such as food & drink, pharmaceuticals and semi-conductors.
Aviation emissions have been included in the scheme since 2012.
Companies participating in the scheme are required to report their emissions to the EPA by March 31 each year.
Dr Tom Ryan, EPA programme manager, said: "Greenhouse Gas emissions from the Emissions Trading sector have been increasing each year since 2013 and in 2016 were the highest in eight years.
"The increase in emissions is a disappointing indicator that the price of carbon remains too low for the trading system to have the desired impact on emissions in Ireland.
"In addition, Ireland has a national policy position that commits us to reducing our carbon emissions by at least 80% compared to 1990 levels by 2050 across the electricity generation, built environment and transport sectors while achieving carbon neutrality in the agriculture and land use sectors.
"In order to deliver on our national policy position we must break our dependence on fossil energy infrastructures. This will take planning, investment and time but can be achieved in the overall framework of national, EU and global commitments."