By Anthony Boadle and Isadora Machado

BRASILIA (Reuters) -Brazil's Congress on Thursday overturned a presidential veto that had struck down the core of a bill to limit Indigenous land claims, setting up a likely clash at the Supreme Court.

Indigenous groups had supported President Luiz Inacio Lula da Silva's veto, while the bill had the backing of the powerful farm lobby.

In a joint session of both chambers, lawmakers voted overwhelmingly to annul Lula's veto of a policy limiting claims to ancestral lands where Indigenous people lived in 1988.

The issue is expected to be decided by the Supreme Court, which ruled in September that the deadline was unconstitutional.

Lula created the first Ministry of Indigenous Peoples when he took office in January and has vowed to recognize pending land claims.

In October he vetoed the core of the bill, a move seen as a major victory for the country's 1.6 million Indigenous people. Many of them have struggled to defend land rights threatened by the advance of Brazil's agricultural frontier into the Amazon region.

The number of land conflicts has increased as Brazil's farm sector has boomed in recent decades into a global powerhouse. Indigenous communities across the country claim land that farmers have settled and developed, in some cases for decades.

The core of the bill that Lula had vetoed sought to, by law, establish a cut-off date for new reservations on lands where Indigenous people did not live on Oct. 5, 1988, when Brazil's Constitution was enacted.

"What happened in Congress is the path to destruction," said Raoni Metuktire, chief of the Kayapo people, in an interview with Reuters.

Metuktire, the Indigenous leader recognized by his large lip plate who has become an international symbol for the fight against deforestation, also called on lawmakers to work to protect tribes.

Brazil's congressional farm caucus, meanwhile, argued that greater legal security would curtail often-deadly land conflicts.

"There is no lack of land for Indigenous people in Brazil. What is missing is support so that they can develop and enjoy the land they already own," said opposition lawmaker Ciro Nogueira on social media.

Indigenous leaders and advocates say protecting their lands is the best way to preserve the Amazon rainforest, which scientists say is crucial to curbing climate change.

Celia Xakriabá, one of only two Indigenous members of Brazil's Congress, called Thursday's vote "a defeat for the climate agenda."

Groups of protesters from some of Brazil's 305 tribes, wearing feathered headdresses with painted faces, danced and chanted outside Congress in support of the presidential veto. Leaders warned that the legislation backed by the farm lobby would lead to more violent conflicts.

Among the protesters, Indigenous Peoples Minister Sonia Guajajara told Reuters she was hoping Lula's veto would stand, because the deadline threatened claims to ancestral lands vital for the survival of Indigenous culture in Brazil.

(Reporting by Anthony Boadle, Isadora Machado and Maria Carolina Marcello; editing by Jonathan Oatis and David Gregorio)