A military statement identified the late officer as regional commander Lieutenant General Sarfraz Ali. It said that, according to an initial probe, the crash happened due to bad weather.
The helicopter was part of relief efforts in flood-stricken Baluchistan, where rain and flash flooding have killed nearly 150 people since June. The military gave no further details.
Pakistani President Arif Ali, Prime Minister Shahbaz Sharif and other senior politicians expressed 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 Baluchistan and Rajanpur, a district in the eastern province of Punjab.
Since June, rains and flash floods across the country have killed nearly 500 people. Since then, rescuers, supported by the military, have evacuated thousands of stranded people, including women and children, from various parts of Pakistan.
More rain is expected this week in Pakistan, where the monsoon season runs from July to September.