The organising secretary of the National Union of Somali Journalists, Ali Moallim Isak, received threatening phone calls after two gunmen arrived at his office only to find that he was not there.
The incident, which occurred on Monday, follows a recent spate of attacks on Mogadishu's intellectual and media elite, according to a statement from Reporters sans Frontieres in Paris.
The statement said the man who threatened Isak by phone said he (Isak) would be killed if he did not stop what he was doing.
Gabriel Baglo of the International Federation of Journalists told Reuters that reporters were being targeted because "their work disturbs some people who claim they are fighting for democracy but ignore the fact that press freedom is one of the bases of democracy".
According to the NUSOJ, at least 13 journalists have fled the country, seeking refuge in Kenya. However, 10 are still stuck at the border as Kenya has restricted visas for Somalis for security reasons.
Omar Faruk Osman, secretary general of the NUSOJ, said in a statement: "We denounce this senseless attempt and baleful message, and will not discourage us to keep on our commitment to defend press freedom. We will continue monitoring and investigating crimes against journalists and media, and as well as abasing criminals."