The Brazilian government sees the dams on the Madeira river, one of the Amazon river's biggest tributaries, as crucial to prevent energy shortages in its fast-growing economy over the next decade.
Beyond that, the $13 billion Jirau and Santo Antonio projects are seen as a key step in regional integration, creating a waterway that would cut transport costs for Brazil's agriculture exports and for farming areas in Bolivia and Peru.
Brazil's new environment minister, Carlos Minc, who has vowed to slash the time taken to license big projects, attached 40 provisions to Monday's approval of the installation of the Santo Antonio dam.
But environmentalists see the dams as a potential disaster that will flood up to 494,200 acres of forest, dramatically changing the ecosystem. They say the government has not provided enough safeguards.
"Minc is blowing a lot of smoke and pretending his agency is demanding a lot of rigorous measures," said Glenn Switkes, Latin America Program Director for International Rivers Network, a California-based group that protects rivers and the communities that depend on them.
"We're dealing with a principal tributary of the Amazon... which has maybe the highest biodiversity of fish and among the highest biodiversity of birds in the world."
Environmentalists said the dams violate the Equator Principles on project finance that were signed by several banks potentially funding the projects, possibly opening the way for legal challenges.
But while conservationists have so far failed to hold up the licensing process, the separate consortiums building the dams have launched into a quarrel that has the government worried about a legal battle and possible delays.
The government threatened to reopen the auctions or take over the projects through state-controlled generator Eletrobras if the business groups did not resolve their differences.
Victor Paranhos, head of the Enersus group that won the Jirau concession, accused the rival group led by construction giant Odebrecht of espionage after it sent a report about Enersus's building plans to the environment agency.
Odebrecht responded by starting legal proceedings that could lead to a defamation case against Paranhos.
The report by Odebrecht was critical of Enersus's plans to move the Jirau dam six miles downriver, something that could affect the other dam's generation capacity. The relocation has not yet been approved by the government.
"If an accord does not happen, the government could take the initiative to build the two works through Eletrobras," Energy Minister Edison Lobao told reporters.
French utility Suez, which leads the Jirau group, threatened last month to stop new investments in the Brazilian power sector if Odebrecht kept up its complaint, raising the prospect of wider fallout from the row.
Any delay in the projects is likely to raise investor concerns about their profitability, already fed by regulatory uncertainty and pressure from Brazil's government for low consumer tariffs.
The Jirau consortium agreed to market electricity from the 3,300 megawatt project at a 21.5 percent discount compared with the auction's base price.
Erasto Almeida, an energy analyst at Eurasia Group in New York, played down the risk of major delays, however.
"The Brazilian government really wants to get these projects done because of concerns about potential power shortages," he said. "My sense of this is that both companies will defend their interests and you might have legal action but there'll be some kind of agreement."
The Santo Antonio consortium also includes an investment fund set up by Spain's Santander and Portugal's Banif, and Furnas, a subsidiary of Eletrobras.