Zulkarnaen was the director of PT Putra Rajawali Banjaran, a state-owned pharmaceutical company, and had been serving as a witness in a corruption case.
Azhar made no comment to reporters as he was led away by police following his arrest.
But he said over the weekend that his efforts to crack down on corrupt politicians and businessmen in the country had earned him many enemies.
Azhar said that he respected the legal process and would cooperate with the authorities.
"I and my family are ready to face this case," he said.
Since its establishment in 2003, the KPK has gained a reputation as one of the few clean institutions in Indonesia.
According to Transparency International, an international organisation which monitors corruption, Indonesia ranks as one of the world's most corrupt countries.