According to the federation, the reigning World Cup champion used the cream bought by her doctor at an Italian pharmacy last month without knowing that it contained the banned anabolic steroid clostebol.
"Johaug has tested positive after using a cream on a sunburnt lip," a Norwegian Ski Federation statement said.
Johaug, who won the first of her two World Cup titles in 2014, has also claimed three Winter Olympics medals, including a gold in the women's 4x5 km relay at the 2010 Vancouver Games, and seven world championship titles.
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"I am devastated and despairing after getting into this very difficult and, for me, unreal situation," Johaug said in a statement.
She said she felt the finding was unfair even though "I am of course aware of the responsibility I have as an athlete for the medicine I use".
Norway's anti-doping agency was expected to decide on any sanctions at a later date, the Ski Federation added.
Earlier this year, Norwegian cross country skier Martin Johnsrud Sundby lost his World Cup and Tour de Ski titles from the 2014-15 season after a mix-up over the administration of asthma medicines.
The Court of Arbitration for Sport (CAS) ruled that Sundby had violated World Anti-Doping Agency (WADA) rules. It also gave him a two-month ban.
(Reporting By Terje Solsvik and Alister Doyle; Editing by John O'Brien)
