"You will go to hell, French journalists," read one of the slogans daubed on the walls of the cultural centre compound, which has been closed since it was damaged in a fire last October.
"Anything but the prophet," read another.
Police were deployed outside the compound's main gate as well as on the adjacent main road, an AFP correspondent reported.
The cover cartoon carried by Charlie Hebdo on Wednesday, in its first edition since an attack on its Paris offices claimed by al Qaeda killed 12 people on January 7, has sparked angry protests across the Muslim world.
Last month, a bomb attack claimed by small ultra-conservative group Jund Ansar Allah caused minor damage to the compound's walls.
Afghan President condemnation
Afghan President Ashraf Ghani on Saturday condemned the decision by French magazine Charlie Hebdo to show a cartoon of Prophet Muhammed (pbuh) on its cover.
Ghani blasted the cartoon as "an insult to the sacred religion of Islam and the Muslim world", a statement from the presidential palace said.
The satirical magazine's new cover has angered many Muslims worldwide, sparking protests from Pakistan to Niger.
"President Ghani on behalf of the Afghan nation condemns this insulting act, and termed it desecrating the religious values," the palace said, describing the magazine's decision to publish it as "irresponsible".
Wednesday's issue of Charlie Hebdo was the first since brothers Cherif and Said Kouachi gunned down 12 people at the magazine's Paris offices on January 7 over such cartoons.
Ghani had strongly condemned the bloody assault on the magazine, branding it "heinous".
There were protests across deeply conservative Afghanistan in 2012 over earlier cartoons by the magazine showing Prophet Muhammad (pbuh), as well as over a US-made anti-Islam film.
A few hundred people demonstrated last week in the central Afghan province of Uruzgan, praising the gunmen and criticising Ghani's condemnation of the Paris attack.
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Funny that the French were trying to appease the Palestinians by supporting their statehood.