General Mohayedin Ghori commanded the 207th Corps and was one of the six regional commanders of the Afghan army, responsible for the country's western zone, defence ministry spokesman Mohammad Radmanish said.
"General Ghori was martyred and a number of officers injured in the crash," Radmanish said.
He said a "technical fault" caused the Russian-made Mi-17 aircraft to go down in the Murichan area of the Bala Murghab district.
Ghori was on a mission to visit a newly established army base in the volatile district, where the Afghan army has recently pushed back a major Taliban offensive.
Taliban insurgents claimed responsibility for the crash in a statement but Radmanish denied this, saying there were no insurgents operating in the area at the time of the accident.
Afghan president Ashraf Ghani described the death of General Mohayedin as a "big loss" for the Afghan security forces and people, according to a statement.
The US-led NATO coalition also issued a statement expressing condolence over the death of the top Afghan general.
A local official who spoke on condition of anonymity said the provincial head of the country's spy agency was among those wounded in the crash.
He could not give details of exactly how many other people had been injured in the accident.
Once a strong flying power thanks to Soviet Union support , Afghanistan's air force was decimated by the civil war of the 1990s and the turbulent period of Taliban-rule.
The Afghan air force (AAF) now has around 100 aircraft, including 27 MD-530 attack helicopters, and about 20 small support aircraft, such as the Brazilian built A-29 Super Tucanos -- used against drug traffickers in Latin America.
It also has approximately 50 Russian Mi-17 transport choppers.