An Afghan police official said all aboard appeared to be American, but the US military would not confirm that or give the nationalities of the passengers.
The US military suggested severe weather brought down the CH-47 Chinook near Ghazni city, 125km southwest of the capital, Kabul, as it returned from a mission in the south.
"Sixteen people have now been confirmed dead in the crash," a military statement said.
Two others listed on the flight manifest, "remain unaccounted for".
The statement said the names were being withheld until their next of kin were informed.
Military spokeswoman Lt Cindy Moore said the helicopter was one of two Chinooks flying to the main US base at Bagram, north of Kabul, when controllers lost radio contact.
A provincial governor said the helicopter went down in Ghazni province, 120km southwest of the capital Kabul, during a heavy dust storm.
"We collected nine bodies. They were all wearing American uniforms and they
were all dead"
Abd al-Rahman Sarjang,
chief of police, Ghazni
"We were first to arrive at the scene," the province's governor, Asad Allah Khalid said, adding that the helicopter was burning when they arrived.
Abd al-Rahman Sarjang, the chief of police in Ghazni, said the helicopter came down at about 2.30pm (1200 GMT) near a brick factory 5km outside the city, and burst into flames.
US troops rushed to cordon the area to look for any survivors, he said.
"We collected nine bodies. They were all wearing American uniforms and they were all dead," Sarjang said.