Embraer officials declined to comment. The company’s U.S. headquarters are in Florida, where the planes for Afghanistan would be assembled.

Embraer still questions why it was stripped of the contract in the first place, according to another person who has direct knowledge of the company’s deliberations on the contract. If the problems were mainly administrative, rebidding the contract “is disproportionate” as a resolution, the person said, adding that suspicions in Brazil are high that the new competition “is tilted in favor of Hawker Beechcraft.”

Hawker Beechcraft hasn’t objected to the absence of a fly-off, but it has other concerns about the bidding process. For one, it thinks the Pentagon has lowered the standards for the aircraft’s ejection-seat system, said Derek Hess, the company’s vice president for light attack programs. That shaves an edge, he said, because Hawker Beechcraft seats accommodate a wider variety of pilots, something the Air Force told congressional staffers in April was unnecessary because only Afghans would pilot the planes.

On Tuesday, Embraer’s partner in the competition, Nevada-based Sierra Nevada Corp., said it had sued the Air Force to have the original contract reinstated. Observers described it as a significant move as the U.S. government is a major Sierra Nevada customer, but the corporation said it planned to continue the competition.

Taco Gilbert, a vice president at Sierra Nevada Corp., said in a recent interview that, “We remain concerned that there is no fly-off. All we have ever asked for is integrity in the process and a fair and open competition.”

Buying planes for the U.S. military and the nascent Afghan air force has been subject to political interference from the beginning. Embraer initially had the support of Army Gen. Stanley McChrystal when he was the commander of international forces in Afghanistan, according to a second congressional staffer. But the program was killed in Congress under pressure from Kansas legislators.

Brazilian politicians also are concerned about the handling of the contract. In an interview at the presidential palace in Brasilia, Garcia said he thought that the initial award of the contract to Embraer “was made strictly under technical criteria” but subsequent developments were the result of “political interference” and “protectionist and political intervention.”

Peter Hakim, the president emeritus of the Inter-American Dialogue, a Washington research center, was also critical. “Not only was it insulting to cancel the contract at the last minute, but the explanation was so thin,” he said. “It made it look like the U.S. can act arbitrarily.”

Shannon, the U.S. ambassador, said that for Brazil, the cancellation of the contract “provoked latent concerns about the confidence we have in them and the confidence they have in us as a long-term partner. So we have been trying to reassure them that we are looking for a defense partnership that can be enduring.”

The U.S., which for decades had assumed the sole responsibility for the Western Hemisphere’s defense, now wants Brazil to assume a greater share of the burden. Brazil, where a military dictatorship reigned until the 1980s, is modernizing its once-discredited military, a process that began during the administration of President Luiz Inacio Lula da Silva.

That modernization has potential benefits for American companies. Brazil bought UH-60L Black Hawk helicopters from Sikorsky Aircraft Corp. of Stratford, Conn. Esterline Corp. of Bellevue, Wash., has a contract to provide equipment to Embraer’s KC-390 military tankers.

While in Rio de Janeiro, Panetta said the U.S. had approved nearly 4,000 licenses a year to export technology to Brazil, “ranging from weapons and aircraft to integrated combat systems for navy ships and submarines.”

“This is on a par with the U.S. government’s license approval rate for treaty allies, for our closest partners,” he said.

A U.S. concern is whether the outcome of the bidding for the Afghan planes will affect a $4.4 billion contract to sell Brazil 36 fighter jets. Boeing is competing with France’s Dassault Aviation and Sweden’s Saab for the deal. It’s unclear whether that contract could be affected if Brazil continues to harbor doubts about the Pentagon’s process for deciding on the Super Tucano A-29 – the pride of the Brazilian air force – for Afghanistan.

“They are humans with sentiments and they have long memories,” a Brazilian official said, referring to the Brazilian military. “I recently met a military official complaining about some slight from 15 years ago.”