The group is believed to be supporters of President Jacob Zuma.
"[The] conference was collapsed [on Friday night] by violent hooligans," provincial spokesperson Makonde Mathivha said.
"Delegates had to flee the venue. It was terrifying."
Mathivha said it was very clear to the party in Limpopo who the people were, claiming that former provincial secretary Joe Maswanganye was part of the group.
"They wore T-shirts with the face of Zuma," he said.
"It's a group refusing to accept the provincial conference [that took place] last year."
Maswanganye was defeated at Limpopo's provincial elective conference last year and replaced by current secretary Soviet Lekganyane.
Mathivha said it was worrying when people within the ruling party could not respect the internal democratic processes.
Limpopo delegates were unable to nominate their preferred candidates for leadership of the party ahead of the national elective conference (NEC) in Mangaung.
Mathivha said Lekganyane was liaising with African National Congress secretary-general Gwede Mantashe to discuss the way forward.
"This will be founded on what the secretary-general decides," he said.
Mantashe said nomination processes in Limpopo had been suspended after Friday night's incident.
He said the national executive committee would meet on Monday to discuss whether Limpopo should convene its nomination conference at another time.
"This will have to be endorsed by the NEC."
Limpopo has battled to get the process of nomination started.
Earlier this week, it had to postpone its nomination conference at the last minute to allow branches to complete branch general meetings.
They were given until Friday to do this. This was also the deadline for nominations set by the NEC.
Mantashe said majority of the ANC's provinces and leagues had managed to hold successful conferences.
"We have three outstanding, Limpopo, North West and Western Cape. There are difficult provinces and we are managing these," he said.
North West was expected to nominate candidates on Saturday afternoon. The Western Cape adjourned its Provincial General Council (PGC) early on Saturday morning without endorsing preferred candidates.
Limpopo's regions differed in their nomination of who should lead the party for the next five years.
Some wanted Zuma to retain his position while others wanted change, calling for deputy president Kgalema Motlanthe to take the reigns. – Sapa