The EPA's Draft National Allocation Plan (DNAP) has for the first time set a limit on the amount of CO2 industries can produce.
Companies breaching this cap will be fined €40 per extra tonne at the end of every year, beginning in 2005.
Some 67.5 million tonnes of CO2 emissions will be permitted in the Republic between 2005 and 2007 and companies will be given individual limits.
More than 100 industrial sites including power stations, cement ceramics plants, paper mills, oil refining facilities, food & drink and pharmaceutical producers are covered by the plan.
Companies with emissions above the cap must either cut their output or buy allowances to produce more. They will be able to buy extra allowances priced at around €12 per tonne from companies with low CO2 emissions.
The EPA is trying to promote renewable energy and is going to give generous breaks to Combined Heat and Power (CHP) plants.
EPA Director General Dr Mary Kelly said: "CHP is a highly-efficient technology for energy production and one in which Ireland lags behind many of our EU partners.
"Global warming is a long-term problem that requires a long-term strategic global response. The allocation process proposed by the EPA will reduce harmful emissions by establishing a price for carbon dioxide."
The country is still failing to reduce high CO2 levels and emissions for 2002 were 29% above what they were in 1990.
This was 16% higher than the Government's target and the country compares poorly with other EU states in cutting CO2.
EPA programme manager Dr Ken Macken said the plan will benefit the environment and help the country to meet its Kyoto obligations.
"I believe our proposals are fair and transparent and take into account the environmental integrity of the scheme and the potential effects on the economy.
However, Green Party Energy spokesperson Eamon Ryan criticised the fact the ESB and the large building materials group CRH were given large emissions quotas.
"Rather than change transport and energy policies to help us meet our Kyoto commitments, the Government plans to buy some four million tonnes worth of emission credits from less developed countries," he said.
The plan was also criticised by the environment group GRIAN who said it favours big business.
"Industry appears to have got all they wanted from the ferocious lobby they mounted on Government during the preparation phase of this plan," GRIAN spokesperson Pat Finnegan said.