Luis Chiriboga, who is also a member of the executive committee of South American confederation CONMEBOL, was among those named Thursday in the latest US indictment stemming from a sweeping investigation of corruption at FIFA.
"I have come voluntarily to cooperate with the prosecution," Chiriboga, 69, told journalists as he surrendered to local authorities.
Prosecutors said a judge had issued a warrant for his arrest and frozen his bank accounts after Ecuadoran investigators opened their own probe in connection with the US charges.
They are Juan Angel Napout of Paraguay and Alfredo Hawit of Honduras, both FIFA vice presidents.
Chiriboga's lawyer said her client may be jailed for up to 90 days during the initial investigation.
"Ecuador does not permit the extradition of its citizens, but it assumes responsibility for investigating crimes, including those that Ecuadorans may commit abroad, to prosecute them here," said Attorney General Galo Chiriboga, no relation to the indicted official.