Health Minister Sharon Blady says the therapy is neither medically nor ethically appropriate.
The practice, also known as sexual reorientation therapy, attempts to change a person's sexual orientation from gay to straight.
Blady says conversion therapy can cause substantial harm to an individual.
She says many health organizations have condemned the practice and it has no place in the heath-care system.
Blady says Manitoba Health will work with regional health authorities and health regulatory colleges to ensure the therapy is not practised.
"The idea that sexual orientation or gender identity can be cured through health-care intervention has the very real potential to damage an individual," Blady said in a release Friday.
"It is the position of the Manitoba government that conversion therapy can have no place in the province's public health-care system.
"As such, fee-for-service professionals should not be billing for this practice under the Manitoba Health Services Insurance Plan."