The main sessions of the UN conference were halted after the protest, which was led by African countries and backed by the G77 group of developing nations.
They accused developed countries of trying to back out of the Kyoto Protocol on carbon emissions.
The group refused to continue negotiations unless talks on a second commitment period to the treaty were given priority over broader discussions on a "long-term vision" for action on climate change.
"This is a walk-out over process and form, not a walkout over substance, and that's regrettable," Australian climate change minister Penny Wong said.
"A range of developing countries have expressed their concerns and acted accordingly.
"This is not the time for people to play procedural games.
"We need to resolve the process issues and get onto the substance."
Yvo de Boer, head of the UN Climate Change Secretariat, predicted the negotiations would get back on track this afternoon.
"The vast majority of countries here want to see the continuation of the Kyoto Protocol," he said.
"I'm not aware that any countries are trying to block anything."
Britain's Climate Change Minister has warned that ministers and negotiators "need to get their act together" to get the talks back on course.
The Kyoto treaty ties the rich countries - but not developing countries - that have ratified it to binding emissions curbs.
"Africa has pulled the emergency cord to avoid a train crash at the end of the week," said Jeremy Hobbs from Oxfam International.
"Poor countries want to see an outcome which guarantees sharp emissions reductions yet rich countries are trying to delay discussions on the only mechanism we have to deliver this - the Kyoto Protocol."
Mr Hobbs was referring to the climax of the conference - a summit on Friday which is due to be attended by around 120 heads of state or government.
Greenpeace added that the negotiations had five days "to avert climate chaos".