The decision was welcomed by United Nations child agency UNICEF, worried at a decline in breastfeeding in Cambodia.
Ambrosia Labs - known in Cambodia as Khun Meada, which means "gratitude of mothers", had been exporting milk from more than 90 Cambodian women for more than two years.
The purchase and export of breast milk must stop immediately, Ngor Hong Ly, a Secretary of State at the Council of Ministers, said in an order on Tuesday.
"Despite how poor and difficult Cambodia is, it's not at a level where we sell breast milk," Ngor Hong Ly wrote.
Ambrosia did not respond to a Reuters request for comment.
On its Facebook page, the company said it put the safety and well-being of donors and customers before everything.
"We work hard to set, and monitor, guidelines to ensure that we are not taking milk out of the infants' mouths," it added.
The post said the company would not accept donations from mothers of infants younger than six months, and that donors should pump milk no more than twice a day.
Breastfeeding of Cambodian newborns during their first six months fell 65 percent in 2014 from 75 percent in 2010, UNICEF said.
"Breast milk could be considered as human tissue, the same as blood, and, as such, its commercialization in Cambodia should not be supported," the agency said in a statement to Reuters.