"The testers came to the team hotel, Horner was not there, he was in the hotel where his wife was staying," a RadioShack press officer told Reuters.
"It's mentioned in the whereabouts form, they got the wrong hotel," he added.
"Horner had changed his hotel. It was the Spanish agency that came on behalf of USADA (the U.S. Anti-Doping Agency)."
An AEPSAD spokesman said the agents had gone to the hotel address provided by the U.S. agency early on Monday.
They checked another hotel but Horner was not there either and AEPSAD did not know his current whereabouts, the spokesman added.
"We do not want to make any kind of judgment about whether this was a violation of the rules as we do not have all the facts," he said.
Horner, who turns 42 next month, became the oldest Grand Tour champion and the first U.S. winner of the Tour of Spain when he sealed victory on Sunday for the biggest win of his 19-year career.
Riders are obliged to provide anti-doping authorities with information about their whereabouts.