The closures have hit Wardak province west of Kabul, where the Taliban have shuttered 42 of the 77 health facilities being run by the Swedish Committee for Afghanistan, the aid group said in a statement.
“Due to this closure, an estimated number of over 5,700 patients are affected on a daily basis,” it said.
Doctors and hospitals have been frequently targeted by both sides during the country's decades-long conflict, and this latest loss follows a raid by Afghan security forces on a clinic last week that left four people dead.
Denying people medical treatment and health services in this way “is an obvious violation of human rights and international humanitarian law”, SCA's country director Sonny Mansson said.
“We demand immediate reopening of all health facilities for the people and we strongly urge all parties involved in conflict to refrain from such actions which deliberately put civilian lives at risk.”
The Taliban have not issued any statement, but the militants have previously closed down health clinics and banned polio vaccination campaigns in areas under their control.
In some areas, insurgents and religious leaders tell communities that vaccines are a Western conspiracy aiming to sterilize Muslim children, or that such programmes are an elaborate cover for Western or Afghan government spies.
Last year, the Taliban warned the International Committee of the Red Cross that the group would no longer protect its workers.
The threat forced the ICRC to significantly scale back its Afghan operations.