A woman and two men were arrested on Wednesday after police raided clinics and homes on the outskirts of Kuala Lumpur.
The woman who was arrested was shown on Al Jazeera's 101 East programme trying to sell a baby to undercover reporters.
The woman's son and a medical assistant who works at a private clinic were also arrested, according to Senior Assistant Commissioner Rohaimi Md Isa, from the Royal Malaysian Police's Criminal Investigation Department.
He told Al Jazeera that police planned to charge the three under the Anti-Trafficking in Persons and Anti-Smuggling of Migrants Act.
"The operation is still ongoing," he said, adding that police hoped to arrest more people involved in selling babies.
Al Jazeera's exclusive investigation, which aired last week, revealed that traffickers and doctors are profiting from the illicit baby trade in Malaysia, where a baby's price can range from about $400 to $7,500.
The woman, who was arrested on Wednesday, told undercover reporters that she was housing 78 pregnant Indonesian women at various locations across Malaysia.
Calling herself "Bonda", or mother in Malay, the woman sent a photo catalogue of pregnant women for potential buyers to choose from.
She offered to sell a baby for $1,500.
"Bonda" guaranteed that the birth mothers would not try to find their babies once they were sold.
"I have dealt with over 1,000 Indonesians with no problems," she said. "They never ask where their children go after giving them up."
Al Jazeera found that those buying babies in Malaysia are often childless couples desperate to start a family and frustrated with the country's official adoption procedures. But activists say some babies end up in the hands of syndicates that force children to beg or groom them for paedophiles.
-Al Jazeera