The FDFA’s Swiss Maritime Navigation Office is responsible for the Swiss merchant fleet. The ships are privately owned. However, the Swiss Confederation may commandeer them for the country’s economic needs in time of crisis or war.

The Swiss Maritime Navigation Office (SMNO) of the Federal Department of Foreign Affairs has administrative, operational and technical supervision as the competent flag state and licensing authority for seagoing Swiss merchant ships, their operators and crews, as well as for recreational and leisure shipping under the Swiss flag at sea. For this purpose, the SMNO, which is based in Basel, also keeps the register of seagoing Swiss yachts and small and coastal vessels, among other things, while the register of seagoing merchant ships (Swiss Register of Shipping) is kept by the Land Registry and Survey Office of the Canton of Basel-Stadt.

The SMNO also represents Switzerland's interests in the field of international shipping in a number of international bodies dealing with shipping, namely the International Maritime Organisation (IMO) in London and the Central Commission for Navigation on the Rhine (CCNR) in Strasbourg. The SMNO employs a small team of 8 technical specialists and lawyers.