Eric Aniva, from the southern district of Nsanje, was held after giving a media interview confessing to have slept with the girls for a fee of between four and seven dollars, paid by each of their families.
The little-known local practice lasts three days and is performed in southern Malawi by men known as "hyenas" at the request of a girl's parents after her first menstruation.
British paedophile gets life in prison for Malaysia, Cambodia crimes
The ritual is believed to train girls to become good wives and to protect them from disease or misfortune that could fall on their families or their village.
"Aniva was arrested on Monday after he was summoned to my office," district commissioner Gift Lapozo told AFP.
In a BBC interview broadcast last week, Aniva confessed to being infected with HIV and sleeping with at least 100 girls without using protection.
"Some girls are just 12 or 13 years old, but I prefer them older," he said.
Sex abuse victim allowed euthanasia in Netherlands
"All these girls find pleasure in having me as their hyena. They actually are proud and tell other people that this man is a real man, he knows how to please a woman."
It was unclear over how many years Aniva had been a "hyena".
Malawian President Peter Mutharika had earlier issued a statement ordering Aniva's arrest and calling for an inquiry into the role of the parents involved.
Aniva should "be investigated for exposing the young girls to contracting HIV and further be charged accordingly," Mutharika added.
"Harmful cultural and traditional practices cannot be accepted."
The sexual cleansing ritual is also performed on bereaved widows in Nsanje district to exorcise villages of evil spirits or to prevent another death occurring.
Aniva, who has two wives and was reported to be in his 40s, said a "hyena" was selected by the community based on good morals and that custom did not allow him to use condoms.
"There was nothing else I could have done," one girl told the BBC.
"I had to do it for the sake of my parents. If I'd refused, my family members could be attacked with diseases -- even death -- so I was scared."
Malawi, which has one of the highest HIV infections in the world, criminalises sex with a person under the age of 16.
If found guilty of underage sex, Aniva could be imprisoned for life.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ