The Electoral Commission of South Africa (IEC) has given the go-ahead for a vote recount in parts of the Western Cape, following complaints from political parties about "missing votes".

The recount is expected to take place on Thursday in certain voting districts. 

The Cape Independence Party, Democratic Independent Party (DI) and DA lodged complaints with the IEC in which they questioned the handling of votes during the 1 November municipal elections.

Cape Independence Party leader Jack Miller told News24 he welcomed the IEC's decision to conduct a recount at 12 voting stations. 

"We actually identified 36 voting stations where there is a discrepancy. We are concerned that only 12 were approved, but we will be taking this further to get the remaining 24 voting stations recounted," Miller said. 

He added that the party would approach the Electoral Court. 

"We will be making sure that our supporters' votes are counted," he said.

In response to the Cape Independent Party's complaint, provincial IEC officer Michael Hendrickse said the commission considered the objection in terms of the Municipal Electoral Act.

"The basis of the Cape Independence Party objection is the alleged widespread confusion in correlating the abbreviated name of the Cape Independence Party namely 'CAPEXIT' as appeared on the ballot papers in the metro, with the name Cape Independence Party as was reflected on the results slips," he added.

"They alleged that a number of votes cast in favour of the Cape Independence Party were not allocated to the party as a consequence of such confusion."

Hendrickse added that on the basis of evidence obtained from the investigation, it was resolved that a recount had to be urgently conducted in the presence of party representatives.

The DA's Matthew Kempthorne, a PR councillor and one of the DA representatives on the IEC multi-party liaison committee, also queried the handling of votes. 

The DA alleged that a number of votes cast in favour of the DA were not allocated to the DA but were inadvertently allocated to the DI.

Kempthorne said the party picked up inconsistencies at two voting stations.

"Basically, what we think happened in the morning [is that] they wrote the DA's results in the DI column and we are double-checking the results," he added.

The recount could affect seat allocations.

Meanwhile, smaller political parties have been calling for a re-election.

DI President Anwar Peters accused the IEC of being untruthful.

Peters said: "The DA is now asking for a recount and now their objection is being entertained. The IEC is there to do a job but it's not doing it. How do we know where these ballots come from? We can't trust them. This is an injustice and an insult and they are attacking our integrity."

Hendrickse said he welcomed the fact that parties followed the legal route in terms of the Act to raise concerns.

"The commission investigated and decided the best way to determine the specific objections with sufficient particularity, as opposed to generalised claims, was a recount in a very limited number of voting districts."