The 32-year-old finished 20th in the men's short race in Lausanne and underwent tests before and after the event.
The post-race exam returned a positive result for erythropoietin (EPO), which increases the body's ability to generate oxygen-carrying red blood cells - improving endurance.
"In the last cross world championships in Lausanne, I passed two anti-doping blood and urine tests, one which was a surprise test as soon as I arrived and another one after the competition, less than 24 hours after the first one," Garcia said in a statement. "Several days after I was notified by the Spanish Athletics Federation (RFEA) that the second test had given positive for EPO.
"I was very surprised and shocked. First due to the positive outcome and substance reportedly found and secondly because of the discrepancy with the first test."
Garcia did not have an explanation for the results, and questioned the methods used by the sporting governing bodies.
"Throughout my sporting career I have undergone many anti-doping tests with the calmness that I have nothing to hide and with the confidence that the systems used by the labs are 100 percent correct," he said. "Now I have discovered that these systems are not correct and frankly I cannot understand how these systems are accepted by sporting organizations,"
Garcia will not compete while he awaits the counter-analysis and the decision by the highest governing body, the International Athletic Federation (IAAF).
The Spanish Athletic Federation will not comment until the IAAF provides official confirmation of the positive tests.
This is likely to affect Garcia's participation in the World Championships held in Paris in August.
Garcia has had a superb year since breaking the European 5000-meter record in February during the European Championships in Gent with a time of 13 minutes, 11.39 seconds.
On Feb. 22 in Seville, he broke the continental 3000-meter indoor record held by legendary Spanish athlete Fermin Cacho, running a time of 7 minutes, 32.98 seconds.
At the World Indoor Championships held in Birmingham on March 16, Garcia finished second in the 5000 meters behind Ethiopian Haile Gebreselassie.