The commander, Nabi Hanfi, was not present at the time of the attack, said Wajid Khan, a local government administrator. Hanfi has been battling the Pakistani Taliban in the Orakzai tribal area where the bombing occurred.
Gunmen first fired shots at Hanfi's compound in Balandkhel village, and then the suicide bomber detonated his vehicle, said Khan. The blast killed 15 people and wounded six others, he said.
No one has claimed responsibility, but suspicion will likely fall on the Pakistani Taliban.
A local tribal leader, Malik Nek Marjaan, said the Pakistani government has been supporting Hanfi's group in its battle against the Pakistani Taliban.
On Wednesday, suspected separatists killed two Pakistani soldiers, in a wave of attacks targeting troops doing relief work in a remote region of the country's southwest where a major earthquake killed at least 376 people last week, military officials said.
Also in southwestern Baluchistan province Wednesday but far from the earthquake zone, a bomb went off at the Pakistan-Afghan border, killing six people and wounding 11 others, said Pakistani security officials.
The attacks on soldiers providing earthquake assistance highlight the difficulty and danger involved in doing such work in an area where separatists have been battling the army for years.
In the first attack, a bomb blast hit a military vehicle, killing the two soldiers, the officials said. The explosion near Mashkay, a village in the province's southwest, also wounded three soldiers. Their unit had been dispatched to the disaster zone after the magnitude-7.7 earthquake rocked the province on September 24.
Later in the day, gunmen carried out four separate attacks against troops delivering relief supplies in the same area and a checkpoint established as part of the effort, said Pakistani military officials. No one was hurt in those attacks, they said, speaking on condition of anonymity because they were not authorized to speak to the media.
There was no claim of responsibility for the attacks but suspicion fell on Baluch separatists who have been battling the Pakistani military for years and have claimed responsibility for similar attacks in recent days.
The military has been ferrying aid into the region by helicopter and evacuating the injured, but their increased presence in a particularly contested area at the earthquake's epicenter has led to renewed clashes.
Awaran district where the quake was centered has been a stronghold of the separatists. Even among Baluchistan residents who aren't part of the armed conflict, there is strong resentment against the central government, which many residents contend exploits the southwestern province's oil, natural gas and mineral deposits.
On Saturday, gunmen killed four Pakistani troops carrying rations for earthquake victims.
Last week, militants fired on two helicopters, including one carrying top government officials surveying the damage. No one was wounded in the incidents.
Wednesday's bombing at the Pakistan-Afghan border took place at a land crossing located in the Pakistani town of Chaman, some 480 kilometers (300 miles) south of the earthquake zone, said security officials.
The six people who were killed were civilians. The wounded included six Pakistani border guards and five civilians, said the officials, also speaking on condition of anonymity because they were not authorized to talk to the media.
No one has claimed responsibility for the attack. In addition to separatists, Baluchistan is also home to Islamic militants who periodically carry out attacks against both civilians and Pakistani security forces.
Associated Press writer Abdul Sattar contributed to this report from Quetta.