Their recommendations go against those of the EU's executive Commission, which said last month it was too early to set post-2012 targets.
A statement agreed by the ministers said developed nations ought to aim for cuts "in the order of 15-30 percent by 2020 and 60-80 percent by 2050, compared to the levels envisaged in the Kyoto Protocol".
The proposals will be made to a meeting of top European leaders later this month.
EU officials said the goals reaffirmed the 25-nation bloc's status as a leader in the fight against global warming.
"I believe that we have demonstrated our ability to play a leading role today," Lucien Lux, environment minister from Luxembourg, which currently holds the EU presidency, told a news conference.
Commissioner Stavros Dimas, who had previously opposed setting targets now to avoid scaring off other countries in climate change negotiations, said the ministers' decision would not hinder talks with countries the EU wants to be more active in emissions reduction.
"The way that the conclusions are formulated will not be an obstacle for bringing on board the United States or other fast developing countries, which are very important for fighting climate change on a global basis," he told a news conference.
The environment ministers said they wanted their countries to "send a strong political message" on climate change.
"The global nature of climate change calls for the widest possible cooperation by all countries and their participation in an effective, cost-efficient and appropriate international response," the statement said.
In February, the European Commission said it would not suggest setting targets now for lowering emissions after 2012, as it focused instead on pulling the United States and some developing nations into the climate change battle.
The Kyoto Protocol aims to cut greenhouse gas emissions by developed nations by 5.2 percent of 1990 levels during the five-year period 2008-2012. The gases are blamed for contributing to global warming.
The ministers did not set targets for the EU itself after that period, speaking instead of developed nations in general. Australia and the United States refused to ratify Kyoto.
Thursday's goals were a relief to environmentalists, who had feared the EU's leadership role on climate change was slipping.
"WWF believes that this was a positive step, and that the European governments have shown that they will continue to take climate change very seriously," said Oliver Rapf, senior policy officer at environmental group WWF.
"One can assume that from that positive signal which they decided now, that the EU will also set itself a very ambitious reduction target for 2020."
Environmental group Greenpeace encouraged the EU to stick to the higher end of the proposed 2020 and 2050 goals in order to prevent global temperatures from rising more than 2 degrees Celsius above pre-industrial levels.