European Commission president Romano Prodi and Swedish Prime Minister Goran Persson said it would be a "tragic mistake" to tear up the agreement and start from scratch.
On Friday, a senior American official indicated to a visiting Japanese government delegation that Washington would propose an alternative plan.
"If certain parts of the agreement prevent the United States from ratifying it, we should negotiate about those parts rather than bury the entire agreement," wrote Mr Prodi and Mr Persson in a joint article in the Swedish regional daily newspaper Goteborgs-Posten.
"In our opinion, it would be a tragic mistake to tear up the agreement and start over from scratch. We would lose time, and that would make us all losers," the pair wrote.
They stressed that the EU remains committed to Kyoto and will ratify the agreement with or without Washington.
World reaction
The decision by the US to abandon the treaty provoked angry reactions across the world.
A Japanese government delegation travelled to Washington to urge the United States to remain committed to the Kyoto agreement.
According to Japanese media, Deputy Secretary of State Richard Armitage outlined the new US proposals at a meeting with the delegation on Friday.
Japan's Kyodo news agency reported that the US substitute plan would differ from Kyoto by seeking the participation of developing nations.
Mr Armitage said Washington would come up with the new framework in time for an international conference on global warming to be held in Bonn in July.
EU push
The 1997 Kyoto protocol calls on industrialised nations to reduce their emissions of so-called greenhouse gasses.
A delegation from the European Union is heading to Beijing after visiting Tehran in continuing efforts to rescue the Kyoto agreement.
Belgian officials described the meeting with officials in Iran, which heads a grouping of 133 developing countries, as encouraging.
The delegation earlier visited Moscow, where it said it had received assurances that Russia remained committed to Kyoto.
Environment ministers from Japan, China and South Korea are meeting this weekend in Tokyo to discuss measures to protect the environment in north-eastern Asia.
The ministers are expected to reaffirm their commitment to the Kyoto protocol.