JAKARTA, Indonesia — Indonesia’s president has instructed his government to investigate one of the country’s darkest periods, the bloody anti-Communist purges of the mid-1960s, perhaps ending decades of official reluctance to confront the military’s killings of hundreds of thousands of people.

One of President Joko Widodo’s most senior ministers, Luhut B. Pandjaitan, said at a news conference Monday night that the president had told him to begin gathering information about mass graves that are said to be scattered across the Indonesian archipelago. Haris Azhar, the head of an Indonesian research organization, said on Tuesday that the government had begun contacting his group and others about the data.

The purges of 1965-66, in which hundreds of thousands of people are believed to have been killed by the Indonesian military and others, have remained an extremely delicate issue for senior government officials, many of whom were generals.

Mr. Luhut, a retired general who is now the coordinating minister for political, legal and security affairs, appeared to cast doubt on the need for an investigation into the mass graves. “The president asked me to find them, if there are any,” he said in his remarks on Monday night.