The International Civil Aviation Organization's global carbon offseting system, the first such scheme for a single industry, is expected to slow the growth of emissions from commercial flights, costing airlines less than 2% of revenues.
Governments from individual countries must still act on their own to put the agreement's limits into effect.
The system will be voluntary from 2021 to 2026 and mandatory from 2027 for states with larger aviation industries. Airlines will have to buy carbon credits, either from competitors or other industries, to offset growth in emissions.
"It's a document arising from compromises and consensus," said Olumuyiwa Benard Aliu, president of ICAO's governing council at a press conference. "That's the way ICAO works."
Aliu said objections by a small number of countries would not derail the plan. With 65 countries covering more than 80% of aviation activity in the voluntary first phases, participation surpassed the agency's expectations, he said, and more countries will likely join after the meeting.
Tensions were centred around developed nations, responsible for most greenhouse gas emissions in the past, and emerging and developing countries that fear tight regulation could curb growth.
Russia and India have said they will not participate in the voluntary phase, and reiterated on Thursday that the deal puts an unfair burden on emerging countries. China has said it plans to join the voluntary phase.
Brazil, which had previously expressed concerns, voiced support for the deal, but it was not immediately clear whether it would participate in the voluntary phase.
The Air Transport Action Group has estimated that offsetting emissions will cost the industry between $US1.5 billion ($NZ2.09 billion) and $US6.2 billion in 2025, depending on carbon prices, and no more than 1.8% of industry revenues by 2035.
The US Department of State, which had long pushed for a deal, said it "puts the industry on a path toward sustainable, carbon-neutral growth."
But because of the voluntary phase and exceptions protecting smaller markets, environmental groups argued the scheme would not meet the agency's goal of ensuring growth is carbon neutral after 2020.
The International Council on Clean Transportation estimated on Thursday that the agreement would require airlines to offset only about three-quarters of growth after 2021, or one-quarter of total international traffic.
"This agreement is a timid step in the right direction when we need to be sprinting," said Greenpeace UK Chief Scientist Doug Parr in a statement.
Airlines lobbied for a global agreement using offsets in the hopes of avoiding a patchwork of national and regional deals that could be costly to comply with and difficult to adhere to.
Talks will continue at ICAO on the technical details of the deal, especially what types of offset credits will be considered acceptable.
Some environmental groups were critical of the deal's reliance on offsets.
"Taking a plane is the fastest and cheapest way to fry the planet and this deal won't reduce demand for jet fuel one drop. Instead, offsetting aims to cut emissions in other industries," said Transport and Environment director Bill Hemmings.
An assembly of ICAO's 191 member states met and approved the deal, which will apply to international passenger and cargo flights, and business jets that generate more than 10,000 tonnes of emissions annually.
The deal comes a day after the Paris accord to fight climate change entered into force. Aviation was excluded from that accord, though the industry produces about 2% of carbon dioxide emissions, an amount larger than produced by some industrialized nations.
With industry expecting passenger numbers to double to 7 billion by 2034, rising aircraft pollution must be curbed to achieve Paris's temperature targets.
Previous negotiations came close to provoking a trade war ahead of the 2013 ICAO assembly as the European Union, which was frustrated with slow progress, ordered foreign airlines to buy credits under its scheme. China and other countries said that violated their sovereignty.
