That extra deal helped appease Warsaw, which currently allows a density of 42kg/square metre.
Earlier in the day Poland, along with Belgium, France, Greece, Hungary, Lithuania and Slovakia held up the deal before holding bilateral talks with the German EU presidency to reach a compromise.
Austria, which supported the earlier stricter proposal, was the only country to vote against the compromise deal, a European source said.
'A good compromise'
Markos Kyprianou, the European health commissioner, welcomed the agreement: "EU consumers have repeatedly expressed concern at the welfare problems than can arise through intensive chicken farming...
"Not only will this result in better animal welfare across Europe, but it should also contribute to improving the health of the birds and the quality of their meat."
Kyprianou admitted that Monday's deal watered down earlier proposals but called it "a good compromise".
The measures must be implemented by all 27 EU member states by June 2010.
Currently no EU norms exist for chicken farming. Only farms with over 500 chickens will be effected by the new rules.