Flores, who ruled the Central American nation from 1999 to 2004, had undergone emergency surgery last Sunday after suffering a stroke.
“We regret the death of President Francisco Flores and we sympathize with his family at this time,” his far-right Nationalist Republican Party (Arena) said in a statement.
“We thank the Salvadorans who have come physically and through their prayers. My father taught us, my brother and me, that you can leave your country when it is happy and triumphant, but when it is under threat, oppressed and bound, you can never leave it. You save it or you die for it. Many thanks to all,” she said.
Flores was accused of embezzling $15 million dollars of aid from Taiwan that was donated after two devastating earthquakes hit the country in 2001.
Prosecutors say he siphoned $10 million dollars to give to his party and kept $5 million for himself.
Flores maintained his innocence and was under house arrest for the charges.