Abdul Zahir Naibzada, who was appointed by President Hamid Karzai last year, said fighting broke out after forces under the command of governor and warlord Ismael Khan, Sadiq's father, attacked his home and his 17th military division headquarters on Sunday.
The ensuing clashes between Khan's forces and Naibzada's troops left between 40 and 50 people dead, a presidential spokesman said.
Khan's spokesman Ghaulam Mohammad Masoon alleged Sadiq was killed by gunmen at Naibzada's house while he was trying to find out who was behind an apparent assassination attempt on his father. He had gone there because a gunman believed to have tried to kill Khan had fled into Naibzada's house, Masoon said.
Naibzada denied the allegation and said he knew nothing about an attempt on Khan's life.
He said Sadiq had tried to storm his home, killed two guards at the entrance, and was himself killed in the subsequent exchange of fire.
"Ismael Khan's forces surrounded the 17th military division and his son, along with the director of intelligence and police security director with 100 troops, surrounded my house at the same time," Naibzada told AFP by telephone.
"Mirwais Sadiq forced the entrance of my residence killing two of my guards, he died in the exchange of fire which followed."
Naibzada said 35 of his soldiers were killed in the fighting and 40 were injured. He accused Khan of later killing the wounded soldiers, saying their bodies had disappeared.
Naibzada fled Herat after Khan's forces took control of the city on Sunday night.
He was speaking to AFP from Karokh, about 40 kilometres northeast of in Herat.
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