Those who incur the biggest penalties are France, Portugal and Spain.
Quotas are normally reduced by a percentage of the amount a nation has over-fished.
Because France, Portugal and Spain repeatedly over-fished the same species in the same area over the last three years, they will in addition see their quotas cut by 50 percent this year compared with their 2011 limit.
Spain faced the largest penalty by volume. For this year, its allowable catch of horse mackerel along its northern coastline is reduced by 11,624 tonnes from 22,409.
Fisheries Commissioner Maria Damanaki said over-fishing would not be tolerated.
"I intend to use deductions to help achieve the main goal of the common fisheries policy: long-term sustainability of Europe's fisheries," she said in a statement.
Since 1983, the EU has sought to manage fisheries by setting the total allowable catch of fish for areas of ocean.
Member states then receive a portion of this number they are allowed to fish based on their traditional catch levels from those areas.
Quotas have been a regular source of contention among major fishing nations such as Spain, Denmark, France and Britain.
Mackerel catches have also been a major sticking point in candidate country Iceland's application to join the EU.
Iceland raised its allowed catch in 2010 for the fish to 130,000 tonnes from about 2,000 tonnes, which brought complaints from Britain and Ireland, who must stay within EU quotas.
The European Union has the third largest fisheries sector in the world after China and Peru, with more than 80,000 EU-registered vessels competing to land Europe's dwindling fish stocks.