For the first time in the Eastern Cape, the ANC has lost its majority in Makana and the Sundays River Valley municipalities.
However, ANC Sarah Baartman regional chair Mabhuti Matyumza, whose region includes both municipalities, said disputes had been escalated to the provincial office over alleged discrepancies in the allocation of PR seats.
In the Sundays River Valley, the ANC got 51.32% of the votes, getting eight of the council's 16 seats.
In 2021, the ANC secured 10 seats after getting 63.52% of the vote.
The party would need the support of at least one additional councillor to secure an outright majority on the council.
In Makana, the ANC secured 31.27% of the vote, translating to 10 of the 25 seats on the municipal council.
In the 2021 local government elections, the ANC won 14 of the 27 council seats, securing an outright majority.
The number of council seats was reduced following changes to municipal boundaries and demarcation between the 2021 and 2026 local government elections.
Matyumza said the ANC retained its majority in Sundays River Valley.
However, he conceded that the party had lost control of Makana municipality.
"If you look at the results in Sundays River, I think it's 51.32%, and it tells you that we still have a majority there," he said.
"That's why we're contesting the one PR seat there, and we've escalated that to the province, to our elections team.
"I think we've done very well under the difficult circumstances.
"We remember the issues of the ANC PR list, which made a lot of people lose appetite."
Matyumza said they were disputing Makana.
The party is challenging the allocation of PR councillor seats, arguing that the IEC's calculations failed to include votes cast specifically for the PR ballot.
According to Matyumza, Makana has 13 PR seats, of which the ANC received 10 and the DA three.
However, Matyumza alleged that the allocation was based on ward results rather than the actual votes cast on the PR ballot.
Matyumza argued that PR seats should have been allocated according to the votes cast on the designated local PR ballot, rather than figures from the ward contests.
He said the ANC believes the IEC may therefore have used incorrect figures in calculating the proportional allocation.
"We are contesting the PR issue. Makana has 13 wards, and out of that, the ANC has received 10 wards, and the DA have received three.
"That is why we have also taken that one directly to the IEC to contest it, because there's no way."
Makana previously had 27 council seats, but following the loss of a ward, the number of wards was reduced from 14 to 13.
Matyumza argues that this should have resulted in a 26-seat council, comprising 13 ward seats and 13 PR seats.
However, the IEC's calculations reflect a council of only 25 seats.
"I don't understand where they are coming in with 25 seats.
"There were 26 seats, and they were gazetted by the minister.
"So even that on its own, it's an error on their side, which I think will also put more weight on what we have faced in terms of our seats candidates in Makana."