The arrest came the day after the Somalian coach of Ethiopia's 1,500 metres world record holder Genzebe Dibaba was detained over an alleged athletics doping ring.
"We understand he (Balla) is in police detention," the government official, who declined to be named as he was not authorised to speak publicly, said on Wednesday.
Spanish police said on Tuesday they had arrested a third person in connection with the investigation but declined to name the person.
Dibaba's Somalian coach Jama Aden and a Moroccan physiotherapist were in police custody on Sunday on suspicion of administering illegal substances to athletes, athletics' world governing IAAF said.
Sudanese-born Balla, 27, became the first Qatari to reach a final at a world championships when he finished sixth in the 800 metres in Beijing last year.
(Reporting by Tom Finn; Editing by Ken Ferris)
