Activists from Animal Rebellion used ladders, ropes and harnesses to climb the Westminster building which houses both the Department for Environment, Food and Rural Affairs (Defra) and the Home Office.
They dropped a a large yellow banner over the entrance of the Marsham Street building reading "COP: Invest in a plant-based future".
The group has vowed to stay put "until the government defunds meat and subsidises a plant-based transition" and pledges to urge all world leaders to do the same when they meet in Glasgow later this week for the United Nations COP26 meeting.
Animal Rebellion wrote on Twitter: "Meat and Dairy is one of the leading producers of greenhouse gases and causes 90% of Amazon deforestation.
"World leaders... cannot talk about meeting the Paris Climate targets and securing global net zero without addressing that our food system is destroying our planet."
Police are currently at the scene with the fire service. No arrests have been made.
It comes a day after more than 50 protesters from Insulate Britain - another offshoot of Extinction Rebellion - were arrested after the climate group re-started its roadblock campaign.
Commuters were targeted during rush hour in the capital as protesters brought traffic to a stop and glued their hands to the floor.
Animal Rebellion spokesperson Nathan McGovern said: “Our protesters climbed the building in the early hours of this morning to send a clear message that we want an end to support for animal agriculture which is killing our planet.
“We will see what the situation with the police is, but the plan is to stay in place indefinitely and this will remain a peaceful protest.”
The entrance to the Defra office was cordoned off by police, with a small group of activists on the ground watching their fellow protesters who posed with their banner on the front face of the building.
Activist Claudia Penna Rojas said: “We are here in the lead-up to COP26 demanding that the government takes drastic action by transitioning to a plant-based food system as the science tells us we need to.”
She acknowledged that “not everyone will be willing to give up meat immediately” but “what we are asking is for the government to be responsible, to stop subsidising animal agriculture – dairy, meat – and begin subsidising more ethical, sustainable ways of farming”.
The Metropolitan Police said in a statement on Twitter: "Shortly after 6am we were alerted to a small group of protestors climbing the outside of a government building in Marsham Street to access the roof.
"Officers are on scene with the London Fire Brigade and are engaging with the protestors".