Spanish anti-doping agency AEPSAD has been declared non-compliant with the WADA code since March 2016.
A delay in updating Spain's anti-doping law has been blamed on a 10-month political deadlock that left the country without a ruling government from December 2015 to October last year.
However, AEPSAD admitted on Thursday that unlike in other sports where international federations had taken over responsibility to carry out drug testing, football governing bodies FIFA and UEFA had refused to do so.
FIFA's jurisdiction is restricted to national teams, whilst UEFA carry out testing only on clubs involved in the Champions League and Europa League, including the likes of Real Madrid and Barcelona.
"The lack of testing in a country with one of the leading football leagues worldwide for a period of almost 12 months is alarming, and will do little to instill confidence in clean sport at a time when it is needed most," WADA said in a statement to AFP.
"WADA encouraged an agreement between AEPSAD and International Sport Federations (IFs) that would ensure testing would be carried out on national level athletes in Spain during the period of non-compliance.
"It is deeply disappointing that some International Federations did not sign the agreement, as this has prevented effective anti-doping programs from being run at the national level in Spain in a number of sports."
AEPSAD said 57 players from Spain's top flight have been subject to tests this season.
However, the validity of those tests is nullified if carried out by AEPSAD's Madrid laboratory due to the agency's non-compliant status.
"The few sporadic checks carried out are therefore without validity," reported Spanish newspaper El Confidencial, who broke the story on Thursday.
The news is just the latest blow to Spain's damaged reputation as a soft touch on doping.
WADA was part of a series of bodies who won an appeal in June against the destruction of 211 blood bags seized in an anti-doping raid on disgraced doctor Eufemiano Fuentes.
The case was a major contributory factor in Madrid's unsuccessful bid to host the 2020 Olympics.