"We mourn the death of president Francisco Flores, and express solidarity with his family at this time," read a message issued from the Twitter account of his rightist National Republican Alliance (ARENA) party.
The announcement of the death of Flores, 56, who led the Central American country from 1999 to 2004, comes as he faced a corruption trial on charges of stealing USD 15 million donated by Taiwan for victims of a 2001 earthquake.
Flores turned himself in to authorities in 2014 to face the allegations, which he steadfastly denied.
