The incidents happened near a military base in Kandahar, and the army said all three victims were shot, with two also hit by grenades.
The victims were identified as Gul Mudin, who died in January, Marach Agha, killed on or about February 22 and Mullah Adahdad, killed on or around May 2.
Military charge sheets detailing the allegations against the men had the names of accusers and officers involved blanked out, and no details were given for the motives that might have been behind the killings.
The soldiers' brigade has seen heavy combat against Taliban fighters, suffering 33 combat deaths and losing three others to non-combat related causes.
Military officials said the next step for the accused soldiers will be what is known as an Article 32 hearing, similar to a grand jury, after which lawyers normally decide whether or not to seek the death penalty in the case.
The announcement of the charges came as high-ranking US military officials faced a Congressional panel on Wednesday, defending the ongoing and increasingly unpopular war effort in Afghanistan.
|General David Petraeus said the war effort was on the right path, despite "setbacks" [AFP]
Robert Gates, the defence secretary, told the Senate Appropriations Committee that it would be a "long and a hard fight" and that US casualties would rise during an upcoming military operation in the country's south.
He added that the conflict was a "roller coaster" of ups and downs but insisted progress was being made.
Gates' comments were in response to criticism from John McCain, a Republican senator, who has voiced deep concerns about progress of the Afghan conflict.
McCain warned the US campaign could be heading toward a "crisis" and expressed scepticism over the July 2011 deadline for a gradual troop withdrawal, given the violence and lawlessness on the ground.
Gates assured members of Congress that the new strategy had put the Afghan war on the right path.
"I think frankly that the narrative ... has been too negative. I think that we are regaining the initiative. I think that we are making headway," he said.
General David Petraeus, who oversees the Afghan war as head of US Central Command, was also grilled by the House of Representatives Armed Services Committee.
|US military officials were questioned by Congress over the Afghan conflict [AFP]
He compared the campaign to a roller coaster ride.
"It is truly an 'up and down' [experience], when you're living it, when you're doing it," Petraeus told the Senate Armed Services Committee
"But the trajectory in my view has generally been upward, despite the tough losses, despite the setbacks."
The second-guessing has touched a nerve in the Pentagon, where some worry negativity is undercutting public support for Obama's strategy before it has a chance to work.
About a third of the 30,000 troops Obama deployed in December have yet to arrive in Afghanistan.
Some of the deepest concerns from Congress centre on the government of Afghan president Hamid Karzai, who raised eyebrows last weekend by firing his interior minister and intelligence chief - two cabinet members widely respected by Washington.
Gates said he had confidence in Karzai, his government and Afghan security forces.
"You know, I read a lot in the press about corruption and so on and so forth. But the reality is there are ministers in Kabul doing their jobs," he said.
"And there are Afghan soldiers and police who are out there dying in even greater numbers than we are fighting for their country."