"Nearly 45% of marriages in this country involve girls below the legal age of 16," the UN Population Fund said in a statement on Thursday.
"The tradition of marrying off daughters as young as six is still common."
The United Nations has also said that it is common for girls to be traded to resolve conflicts between tribal families and that such children usually become the "property of the family or individual who receives them".
The UN agency also announced it was organising a workshop later this month for Islamic leaders from around Afghanistan to try to combat the problem.
Since the fall of the Taliban government in 2001, millions of girls have returned to school and women returned to work, especially in the cities.
A new constitution enshrines women's rights, but the law is often ignored and President Hamid Karzai's US-backed government has little authority in some areas, especially remote rural ones, to enforce it.
US soldier killed
Meanwhile, on the ground, anti-government fighters have clashed with international forces in eastern Afghanistan, killing a US Marine and an Afghan government soldier, during a drive to flush out Taliban-led rebels from a volatile region before key elections, the US military said on Friday.
The clash, in which four Afghan soldiers were also wounded, happened near Asadabad in the eastern province of Kunar, and came as American casualties mount and violence escalates in the run-up to the 18 September vote for a new parliament and provincial assemblies.
On Thursday, the US military reported a roadside bomb killed two US soldiers and wounded two others who were protecting road workers on a US-funded project in southern Kandahar province, a former Taliban stronghold.