Francisco Flores in 2015. (© Stringer. / Reuters/Reuters)

Francisco Flores, a former Salvadoran president whose five years in power were tarnished by accusations of corruption and elitism, died Jan. 30 in the capital city of San Salvador. He was 56.

The cause was a cerebral hemorrhage, said officials with his political party, the conservative Nationalist Republican Alliance, better known as Arena.

Mr. Flores, who led El Salvador from 1999 to 2004, was under house arrest on charges of embezzlement and illegal enrichment. He was accused of diverting more than $15 million, which Taiwan had donated to help the victims of earthquakes in 2001. A court said $10 million of that went to the party backing him and the remainder to him.

Loyda Robles, one of the plaintiff lawyers against Mr. Flores, said last week that his death would end the criminal prosecution, but that the civil litigation would continue.

Robles also said plaintiffs had asked the country’s Supreme Court to add the charge of money laundering to the case. That could expand the criminal prosecution beyond Mr. Flores to include the possible involvement of others.

Mr. Flores had a meteoric rise to the presidency, but once there gained a reputation for being arrogant and distant. He became El Salvador’s first president to be charged and put on trial for acts of corruption during his time in office.

“The people will remember him for the terrible dollarization, for the Firm Hand [to combat crime] and as corrupt,” said Angelica Rivas, who works with a nonprofit organization promoting women’s rights.

Jeannette Aguilar, of the University Institute of Public Opinion at the Central American University Jose Simeon Canas, said various studies showed Mr. Flores’ presidency to be among the worst based on public opinion.

“He was a leader with an arrogant style, a lot of hubris, not close to the people, who responded to the interests of the economic elite who at that time dominated Arena,” Aguilar said.

Francisco Guillermo Flores was born in Salvadoran city of Santa Ana on Oct. 17, 1959, and grew up in a well-off, conservative and anti-communist family. He married Lourdes Rodriguez, and they had two children. A list of survivors was not immediately available.

Mr. Flores rose quickly through the ranks of Arena, which ruled El Salvador between 1989 and 2009. Mr. Flores was still in his 20s when he started in the government of Arena’s first president, Alfredo Cristiani, in 1989.

Just a few days into his new position, a guerrilla attack killed his wife’s father. In the 1990s, he served as an Arena legislator and in 1997 was elected president of the legislature.

He won the presidency in 1999, beating former guerrilla commander Facundo Guardado.

Mr. Flores took office at the age of 39 as Arena’s third consecutive president. He left office in 2004.

During his time in power, El Salvador was hit with successive natural disasters.

Earthquakes in January and February 2001 killed more than 1,000 people and left 200,000 homeless. Later, a severe drought destroyed coffee crops.

The corruption scandal and alleged theft of the earthquake-relief funds sealed his reputation with many. The switch to the U.S. dollar as the country’s currency also received a huge popular backlash.

Salvadorans were encouraged to see the attempts to bring Mr. Flores to justice, but he did not live long enough to see out the process.

“Our justice system has been slow, has obeyed the interests that do not obey the interest of justice of the people and some try to make him out to be the victim,” said Miguel Montenegro from the El Salvador Human Rights Commission.

— Associated Press