Captain Ramotswedi Ngakane of Itsoseng, near Lichtenburg, claims he was assaulted when he demanded his children back from a local pastor.
Ngakane, 38, says he returned from peacekeeping duties in the Democratic Republic of Congo a week ago to find that his children were living with the pastor of the Grace of God is Power Church.
He also alleges that his children were physically and emotionally abused by his former church leader.
Ngakane claims that on Saturday he was assaulted with bricks, garden forks and sjamboks by Pastor Mmatli Mmokwa and some members of the church when he tried to rescue his children, who were given to the church by his wife.
He says his estranged wife, Matshediso, did not only give his children to the church two years ago, but also their household goods and his brand new car.
"I was led to believe that I was possessed by demons and if I donated my earthly possessions to the church my soul would be purified.
"But the pain and suffering my children endured at the hands of the pastor and his wife made me realise that I should not have let them go in the first place," said Ngakane.
He added that his wife gave the church their R17000 savings.
Ngakane has laid assault charges against Mmokwa.
Mmokwa confirmed that he assaulted Ngakane but insisted he had only used the whip to discipline him.
"The man has no morals; his new girlfriend went right inside my bedroom when they brought his children's school uniforms.
"I had to show him that this is my house and no man may disrespect it," Mmokwa said. "We gave the children shelter because they had nowhere to live."
Ngakane said: "Mmokwa is a blatant liar, I have a townhouse in Mmabatho and my parents and my in-laws have houses. My children can choose wherever they want to live."