The Law of Telecommunications was signed during his presidency of the Legislative Assembly in which the former gubernamental ANTEL was sold to two societies in the Private Enterprise. This was signed with the approval of the deputies of the ARENA, PCN and PDC political parties imitating the Neoliberal system that supports the administration of gubernamental agencies by the private enterprise for overall improvement of the coverage in telecommunications.
On March 29, 1998, ARENA announced Flores as their candidate at the presidential elections of the following year. He was considered a moderate within the party.
At the age of 39 (the youngest chief executive of the continent at that time), Flores became the third consecutive president from ARENA by winning an outright majority on the elections in March 1999, and took office on July 1, 1999. He served his five-year term, and was succeeded by another of member of his party, Antonio Saca, in July 2004.