Marry Mubaiwa, 38, who is the wife of Vice President Constantino Chiwenga, 63, was arrested last month on allegations of attempted murder, fraud and contravening currency laws by transferring about $1 million abroad.
She was freed on bail on Monday after three weeks in jail.
According to an affidavit filed Thursday, she has not seen her children, and troops have barred her from their matrimonial home.
The businesswoman and former model wants the courts to urgently order the vice president to hand over their children, aged eight, seven and five.
She said the children “have unlawfully (been) taken away from my custody”.
“I’m not aware of their location nor have I been allowed to see them.
“Not only is this an act of unconscionable cruelty, but it is also brazenly illegal,” she said.
The attempted murder charges against her arose from a trip last year when she accompanied her husband who was airlifted for medical attention to neighbouring South Africa.
In Pretoria she allegedly took the ailing Chiwenga to a hotel, refusing to take him to the hospital until his aides forced their way and took him to a clinic.
Prosecutors alleged that Mubaiwa went to Chiwenga’s hospital ward and asked his security aides to leave saying she wanted to have a private conversation with her husband.
Alone with the bedridden Chiwenga, Mubaiwa allegedly removed an intravenous line and a catheter from her husband causing him to bleed profusely, the prosecution said.
Chiwenga, who led the 2017 ouster of long-time ruler Robert Mugabe, went to South Africa to seek emergency medical attention for a constricted oesophagus, before being transferred to a Chinese hospital where he spent four months.
Prosecutors also said between 2018 and May last year, Mubaiwa transferred money from her foreign currency account in Zimbabwe to South African bank accounts under the pretext of paying for goods to be imported from that country.
She allegedly used part of the money to buy a house in a Pretoria plush golf estate and two luxury cars.
A trial date has not been set yet but she is due back in court on January 14 for a routine pre-trial appearance.