A military statement identified the deceased officer as the regional commander, Lt. Gen. Sarfraz Ali. He said that according to an initial investigation, the accident happened due to bad weather.
The helicopter was part of relief efforts in flood-hit Balochistan, where rains and flash floods since June have killed nearly 150 people. The military provided no further details.
Pakistani President Arif Ali, Prime Minister Shahbaz Sharif and other senior politicians offered their condolences to the families of the victims.
Pakistan is currently using helicopters and boats to evacuate flood victims from various parts of the country, including Balochistan and Rajanpur, a district in the eastern province of Punjab.
Rains and flash floods have killed at least 478 people across the country since June. The downpours also completely destroyed or damaged nearly 37,000 homes in flood-affected areas, according to a report by the National Disaster and Management Authority.
Army-backed rescuers evacuated thousands of stranded people, including women and children. More rains are expected this week in Pakistan, where the monsoon season runs from July to September.