The Burundi investigation is likely to focus on evidence of extrajudicial killings, disappearances, arbitrary arrests and detentions, torture and sexual violence in the two-and-a-half years since Mr. Nkurunziza forced and intimidated his way into a third term in office.

In September, a United Nations human rights panel found that Burundi’s top leaders and security agencies were implicated in such crimes, and it urged the International Criminal Court to open an inquiry.

Rights advocates welcomed the announcement by the court on Thursday.

“The decision of the I.C.C. is a relief for the victims and a real beginning of the end of impunity in Burundi,” said Lambert Nigarura, president of the Burundi Coalition for the I.C.C. “From now on the authors, co-authors and accomplices of the crimes must understand that the games are over.”

Param-Preet Singh, associate international justice director at Human Rights Watch, said Mr. Nkurunziza’s loyalists in the country’s security forces and the police had a “devastating track record of unchecked abuses” that had invited scrutiny by the court.

“I.C.C. involvement means victims in Burundi and their families may one day see those responsible brought to justice,” she said.

Some lawyers and human rights activists have said that the court’s prosecutors were obliged to make good on their planned investigation of Burundi, and needed to send a signal that leaving the court was not a guarantee of immunity.

But court officials concede that experience has shown that leaders in power can effectively block investigations. Whether the investigators can do their work if the government thwarts them remains an open question.