"These acts disturb us. Our anxiety is heightened by the fact that mosques, schools and other buildings related to our religion are desecrated almost every month," the office of Grand Mufti Mustafa Alish Hadzhi said in a statement.
The 45-year-old cleric appealed to the Bulgarian government to take urgent measures to find the culprits of the graffiti, which was apparently sprayed on the facade of the building Friday night, it said.
About 12 percent of Bulgaria's population of 7.6 million is Muslim, the latest census conducted in 2001 showed.
The 90-percent Christian Orthodox country, which joined the European Union in 2007, also has the largest Turkish minority in the bloc -- at about 10 percent.
Güncelleme Tarihi: 18 Şubat 2008, 20:15
The Muslim population also comprises a small group of Bulgarians who converted into Islam during the country's five-century Ottoman rule. Certain gypsies have also declared themselves Muslims.
But Bulgaria's ethnic and religious minorities have lived peacefully since the fall of Communism in 1989. The Turkish minority party Movement for Rights and Freedoms is now a major coalition partner in two successive governments since 2001.
But in 2005, the ultra-nationalist Ataka party also made its appearance on Bulgaria's political scene, running in general elections on slogans like "Against the Turks in the government." Today, it has 11 deputies in the 240-seat parliament.
And Ataka leader Volen Siderov challenged incumbent President Georgy Parvanov in a run-off ballot in 2006.
Bordering on Serbia and very close to Kosovo, Bulgaria recently declared it "will not be among the first to recognise the independence" of Kosovo, largely Muslim province.