Mr. Joko was elected in 2014 on a promise to deliver honest and effective governance in one of Southeast Asia’s most corrupt countries. His latest actions, however, show his inability to withstand pressures from the entrenched elite.

Despite outrage among members of the media and voters over the Budi nomination, Mr. Joko dithered for weeks over what to do. The result has been a distracted government and growing doubts about his competency and commitment to reform. “Imagine the chief of national police as a suspect,” Mr. Abraham said in an interview last week when he still had his job.

The problem goes beyond a single bad nominee. In fact, “there are few institutions in this country that are not riddled with corruption from top to bottom — police, courts, Parliament,” one senior diplomat in Indonesia said. Tensions between the commission and the police are evolving dangerously. In a move widely seen as retribution, the police recently arrested Mr. Bambang and accused him of forcing a witness to provide false testimony under oath when he was a lawyer in 2010. Criminal complaints have also been raised against Mr. Abraham.

Some experts say the legal moves, especially against Mr. Bambang, who has an outstanding reputation for integrity, appear to reflect an intent among the police and their allies to destroy the anticorruption agency. Commissioners and their staff members have also been threatened more systematically than ever before, including with bodily harm, Mr. Abraham said. In in a televised address on Wednesday, Mr. Joko showed little understanding of what’s at stake when he urged “harmony” between the police and the commission.

Reducing corruption in Indonesia is critical if the country is to grow as quickly as Mr. Joko says it must to meet the needs of its people. Commission officials say their prosecution actions have returned millions of dollars to state coffers. Transparency International, which annually rates countries on corruption in their public sectors, says Indonesia has improved its performance on the organization’s “corruption perception index” from 1.9 in 2003 to 34 in 2014; a score of 100 means the public sector is very clean. But Indonesia still ranks 107th out of 175 countries. For comparison, China is 100th on the list of nations, and Russia is 136th.