Police and fans clashed during Zambia’s 1-1 draw with DR Congo after Ebola screening delayed entry to the ground in Ebebiyin.
There were also clashes during Ivory Coast’s draw with Guinea and Mali’s tie against Cameroon on Tuesday in Malabo.
Despite the wait to enter stadiums, Equatorial Guinea Football Federation president Andres Jorge Mbombio claims the threat is contained.
“When we decided to host the tournament, we increased the preventive measures, so that now we can say everything is under control,” he said.
“We feel proud and reassured, and only want to think of football.”
A World Health Organisation (WHO) worker who was conducting Ebola screening at Tuesday’s Group D games told the BBC that there were isolated incidents of fighting between police and fans, with one involving up to 300 people.
The WHO worker says she feared for her safety and had to come inside the gates to carry out the checks for Ebola. The police used electroshock weapons, batons and cattle prods to stop the fighting, after fans surged towards the gates, reports the BBC’s Alex South in Malabo.
Equatorial Guinea are hosting the tournament after Morocco’s request to postpone the event because of the possible spread of the disease was rejected by the Confederation of African Football (Caf) in November.
Supporters have their temperatures checked and are then asked to clean their hands with sanitising gel as they enter stadiums, which is resulting in long queues.