The meeting on Tuesday comes after Amcu president Joseph Mathunjwa fired a broadside at the government over the decision, saying it was political.
Mathunjwa also said the decision is suspicious as it was preparing for a round of wage negotiations in the platinum belt in the coming weeks.
Other than meeting Molefe this week, Amcu could lodge a court application to force the government to back down on its decision.
However, Amcu said its lawyers were going to look into the matter on whether to take it to court.
Mathunjwa said it had been taken aback by the decision by the government despite assuring the Department of Labour that they were going to meet the requirements of holding their conference in time.
The department had issued a notice in the Government Gazette that Amcu was going to be deregistered because it had ceased to be a union.
It said the union had failed to hold its conference as its constitution requires a conference be held every five years.
The department said the last conference was held in 2013 and Amcu had not indicated when its next conference will be held.
Mathunjwa said it was within the time frame to hold the conference this year and accused the department of taking a hasty decision.
The department could not be reached for comment on the meeting with Amcu on Tuesday.
Other political parties have also said the decision by the government to deregister Amcu was to ensure that it was removed from the sector.
Mathunjwa said the decision to meet with the registrar of labour relations on Tuesday was to resolve the matter amicably.
Amcu has been involved in a number of strikes in the past few years.
The union was involved in a protracted strike at Sibanye-Stillwater mine, which lasted for more than five months.
The strike was only resolved about a week ago.
Amcu has been mobilising in the mining sector for some time and the department said it had not held the conference over the past few years and was therefore in violation of its constitution.
Mathunjwa denied there was anything wrong with their finances as it has been alleged by some in public.
He said even the registrar of labour relations never mentioned the issue of funds in the notice to deregister them.