A Taliban spokesman claimed the two-hour attack targeted a US base next to the compound of the Voluntary Association for the Rehabilitation of Afghanistan in Delaram, a town in the western province of Farah, and began before dawn.
The aid group's director, Najmuddin Mujaddidi, said two guards of the agency were killed along with another working for an Indian firm that shared the compound.
He said one of his guards was missing and three working for the Indian firm upgrading the town's main road link were critically wounded.
He declined to name the Indian firm.
Taliban spokesman, Abd al-Latif Hakim, confirmed that they had carried out the attack, but said the intended target was a military post next to the aid agency compound.
Heavy machine guns
Mujaddidi said 20 fighters took part in the attack about 620km southwest of the capital Kabul.
An official of the Afghanistan NGO Security Office said as many as 40 fighters could have been involved.
The Taliban has declared war on
Karzai's US-backed government
"They fired heavy machine guns and rocket-propelled grenades," Mujaddidi said.
The Afghan aid agency has been running agricultural projects in Farah, funded by various UN agencies, since the 1990s and has been attacked in the past by suspected Taliban supporters.
The Taliban movement has declared war against US-led foreign forces in Afghanistan, President Hamid Karzai's government, and local and foreign aid workers.
More than 1000 people, including dozens of aid workers, have been killed in violence since August last year that has severely disrupted aid work in the south and east where the Taliban and their allies are said to be most active.
The Taliban allegedly vowed to disrupt presidential elections held last month and won by US-backed incumbent Hamid Karzai, but these passed off relatively peacefully.
However, the group has stepped up attacks lately.
Last Wednesday, two US soldiers were killed and one wounded in a blast caused by an improvised bomb while they were on patrol in central Afghanistan.
Three German peacekeepers
were slightly injured on Friday
Three German peacekeepers were slightly hurt on Friday when a similar device exploded near their vehicle in the northern town of Kunduz.
Last Tuesday, three foreign UN workers, who had helped run the presidential election, were freed from nearly four weeks in captivity, an incident that raised fears among the foreign community of a wave of Iraq-style kidnappings.