Tests conducted at the Spanish athletics championships in July returned three "adverse analytical findings", the head of the country's anti-doping agency (AEPSAD) told the lower house of parliament on Thursday.
AEPSAD President Ana Munoz did not reveal the names of the athletes but said their licences have been suspended while the correct procedures are followed.
Two of the substances detected carry lengthy bans according to World Anti-Doping Agency (WADA) rules and the positive results have been confirmed by the WADA-accredited laboratory in Lausanne, Switzerland, she added.
The tests were the first conducted by AEPSAD since it was granted wider powers in new anti-doping legislation.
The law was part of Spain's effort to dispel a perception it is soft on doping, seen as one reason for the failure last week of Madrid's bid for the right to host the 2020 Olympic Games.
The country's image suffered a blow in April when the judge in a high-profile doping trial ordered blood bags that could implicate drug cheats to be destroyed.
The Spanish doctor at the centre of the case, Eufemiano Fuentes, had told the court he had clients in cycling but also in sports including soccer, tennis, athletics and boxing.
Fuentes, who denied doping, was given a one-year prison term for endangering public health but the judge's ruling on the blood bags prompted widespread condemnation.
Anti-doping authorities have appealed her decision and Munoz told parliament the blood bags were still in existence pending the outcome.
"Obviously every time an adverse finding comes to light which could lead to a severe punishment it is a reason for sadness," she said.
"Because it means that there is an athlete who did not want to respect the rules.
"At the same time, it is a sign that work well done ... bears fruit."