Spanish sports minister Juan Antonio Gomez confirmed that a "B" test on the German-born skier, who was stripped of a gold medal on Monday, has come out positive as well.
The test means that Muehlegg could be in line for a two-year ban from the sport.
The World Skiing Federation (FIS) and the International Olympic Committee (IOC) have been informed of the results.
Muehlegg tested positive for darbepoetin on Sunday - which is similar to the banned blood-boosting agent, erythropoietin (EPO) - and was stripped of the 50km title he won on Saturday.
But because the test took place out of competition on 21 February, he will retain the gold medals he won in the 10km and 30km events earlier in the Games.
The 50km classical gold has now been handed to Russian Mikhail Ivanov, who originally finished second.