Prosecutors have said they will seek the death penalty in what they say was a case of premeditated murder.
In court on Thursday Azhar shook his head in disbelief when the charges were read in court.
"I will expose everything… The day he was murdered, I was in Australia"
"I object to all the accusations," the former chief of the Corruption Eradication Commission (KPK) told the South Jakarta district court.
Speaking to reporters outside the court Azhar said he was optimistic he would be cleared of all charges, adding he believed he had been framed.
"I was not involved, 1,000 percent. There's a big scenario behind this case, related to my position as the head of the KPK," he said.
"I will expose everything… The day he was murdered, I was in Australia," he added.
The case has thrown the work of the KPK into turmoil after taking on scores of officials, from central bankers to government ministers, in recent years.
In June, the father-in-law of the eldest son of the Indonesian president was jailed for embezzling millions of dollars from the central bank, following an investigation led by the KPK.
But despite recent prosecutions, independent corruption watchdogs such as Transparency International continue to rate Indonesia's among the most corrupt countries in the world.