The New People's Army lobbed a grenade at soldiers guarding a village festival, but it bounced off netting and into a courtyard where the circus was performing.
The local command of the Maoist guerrilla group said it was taking responsibility for the September 1 carnage in the Paquibato district outside the southern city of Davao.
"The NPA issues this self-criticism to apologise to the public and the families for the scores of casualties, including children," a rebel statement circulated to local reporters said.
The insurgents, waging a decades-old Maoist insurgency that has claimed thousands of lives across the Philippines, pledged to compensate the victims and to mete unspecified "disciplinary action on the responsible unit".
The attack left 47 civilians with shrapnel wounds, including four who remained in hospital a week later, military spokesman Lieutenant-Colonel Lyndon Paniza told AFP. No circus performers were hurt, he added.
He said it was not the first time the Davao NPA had attacked civilians, citing a roadside bomb attack by the rebels on a military truck near Davao early last year that killed three civilians who had hitched a ride.
But he said it was the first time the group had apologised for such an incident.
President Benigno Aquino re-opened peace talks with the communists in February last year but the negotiations have been delayed by rebel demands for the release of detained comrades.