By Paulo Trevisani And Djania Savoldi 

BRASÍLIA--Brazil's newly elected Congress was sworn in Sunday and gave a black eye to President Dilma Rousseff, electing a lawmaker largely seen as opposed to her administration for a key position in the legislative body.

Federal Deputy Eduardo Cunha, from the Brazilian Democratic Movement Party, or PMDB, was elected with 267 votes to be the speaker of the 513-member Chamber of Deputies for the next two years. He beat Arlindo Chinaglia, from Ms. Rousseff's Workers' Party, or PT.

Political observers say Mr. Cunha is likely to make it harder for Ms. Rousseff to push her new agenda of economic belt-tightening through Congress.

The position also holds sway over congressional probes likely to be created to investigate an embezzlement scandal involving Brazil's state-controlled energy company Petróleo Brasileiro SA., or Petrobras. The case threatens to engulf Ms. Rousseff's Workers' Party, or PT.

Mr. Cunha's victory "makes it harder [for the government] to adopt certain measures. The cost of negotiation gets higher," said political scientist Paulo Carlos Calmon, from the University of Brasília.

The speaker can dictate how fast bills get voted on, and determine how much space opposition lawmakers will have at commissions specially created to make investigations.

All that said, the government still holds a large majority in both houses, and Mr. Cunha's PMDB is the party of Brazilian Vice President Michel Temer and a top ally of the PT.

The PT tried to strike a deal with Mr. Cunha's camp to have the two parties take two-year turns leading the Chamber of Deputies, Minister of Institutional Relations Pepe Vargas, who is the president's liaison with Congress, told reporters Sunday after the vote.

A spokesman for Mr. Cunha said the deal was rejected because Mr. Cunha was certain he would win.

Mr. Cunha's election is the closest thing to a victory the minority opposition could have hoped for, since he has a track record of opposing bills dear to the government, and has sought to portray himself as independent from the Rousseff administration.

"We never spoke of [making] opposition, but of keeping the House independent", Mr. Cunha said in a speech before the vote.

His victory comes as Ms. Rousseff is hard-pressed to cut government spending and increase taxes. Brazil's once-highflying economy has been bogged down by high inflation and low economic growth, combined with a widening budget deficit that reached 6.7% of gross domestic product in 2014.

In December, for instance, a presidential decree made it harder for workers to get jobless-insurance payments, potentially saving Treasury funds. The new Congress soon will vote on whether that measure can stay in place, and local media reports have said lawmakers likely will change the measure to reduce workers' losses--and Treasury savings.

The economic hardships have cast a pall over Ms. Rousseff's second term. She was re-elected in the October general elections by a thin margin that emboldened the opposition. A more belligerent Congress could make it harder for the president to pass needed overhauls to fix the economy, analysts say.

The legislature was elected in October and sworn in Sunday, right before the speaker vote. Analysts say the government has more influence over the 81 senators, but the lower house has grown more independent in the past few years.

Sen. Renan Calheiros was elected as speaker of the Senate. He is a longtime loyalist to Ms. Rousseff and to her predecessor and mentor, Luiz Inácio Lula da Silva.

The speaker of the Senate also presides over matters that require joint decisions by both chambers, which means Mr. Cunha's powers often will be curbed by hierarchy.

Still, he has enough power to be a thorn in the side for the administration.

Mr. Cunha "isn't easy," said a high-level aide to Ms. Rousseff.

Write to Paulo Trevisani at paulo.trevisani@wsj.com

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