Motaung is accused of forgery and fraud in connection with the construction of the Mbombela Stadium ahead of the 2010 Fifa World Cup.
Hawks spokesperson Colonel McIntosh Polela said two men were arrested on Wednesday for alleged fraud relating to the building of the Mbombela Stadium in Mpumalanga.
"We have arrested two men, one in Naturena and one in Cape Town.
"We are looking for the third suspect," McIntosh Polela told Sapa.
He said the men were arrested on allegations that they forged SA Revenue Services (Sars) documents to obtain a contract to build the Mbombela Stadium.
The project has been dogged by controversy.
Mbombela municipality speaker Jimmy Mohlala, who blew the whistle on alleged corruption in a 2010 construction project, was shot dead in his Nelspruit house in 2009.
Mohlala has accused Mbombela municipal manager Jacob Dladla of manipulating 2010 construction contracts.
Mohlala was also already investigating a fraud case involving a company belonging to Motaung that was responsible for the construction of the Mbombela Stadium.