An autopsy conducted on three of the boys indicated they suffered from gangrene which resulted in renal failure.
The arrests were made in different parts of the province since May, Colonel Sibongile Soci said on Tuesday.
Thirty initiates had died in the province during the current initiation season, the provincial health department said on Sunday.
Department spokesperson Sizwe Kupelo said in the most recent case of botched circumcisions during the initiation season, 10 initiates were rescued from a forest in Mbizana.
"The 10 initiates' private parts are rotten. They are badly damaged. Their condition is scary," he said.
They were recovering in hospital.
A total of 293 initiates are currently in hospitals in the province, and are recovering from dehydration, gangrene and septic wounds. Some had lost their genitals.
'Crack down on this growing problem'
ANC spokesperson Jackson Mthembu said illegal initiation schools were criminal activities masquerading as respected customs.
"Activities that have led to the deaths of initiates, particularly in the Pondoland region of the Eastern Cape, must be harshly condemned," he said in a statement.
In some illegal schools, young men had been taken by force and money had been demanded from their families.
"The justice, crime prevention and security cluster must consider … the establishment of a specialised unit to crack down on this growing problem and halt it decisively in its tracks," he said.
He said those who were arrested had to be speedily prosecuted and the cases hastily concluded. – Sapa