Dobri Karamarinov said the 26-year-old tested positive for the banned steroid drostanolone at the European indoor championship in Gothenburg in March.
Naimova, who won the gold medal in the 60 metres sprint in 7.10 seconds - her personal best, has been temporarily banned by the federation.
"The Bulgarian Athletics Federation has a clear and firm policy against doping, which we followed for years," Karamarinov told reporters. "I"m sorry for what happened to Tezdzhan and I hope she'll provide a rational explanation."
Karamarinov said Naimova, who also won two gold medals at the world junior championship in Beijing in 2006, has two weeks to respond.
In 2009, Naimova was banned for two years for manipulating a doping sample. She was ruled to have tampered with her urine sample at an International Association of Athletics Federations (IAAF) out-of-competition test in Sofia.
If found guilty, Naimova will be forced to return her gold medal from Gothenburg where Ukraine's Mariya Ryemyen came second, France's Myriam Soumare was third and Bulgaria's Ivet Lalova came fourth.
- Sports & Recreation