The Prefecture's predecessor is the ports service founded by the first autonomous Argentine government in June 1810, six years before Argentina declared independence.

The first commander of the force was Colonel Martín Jacobo Thompson, a Porteño of partially English descent who had served against the British in the invasions of 1806–7.

Two PNA patrol vessels, Islas Malvinas (GC-82) and Rio Iguazu (GC-83), were sent to provide an Argentine coastguard service to the islands.

The sortie was actually carried out by two Sea Harriers of 800 Naval Air Squadron, Nº XZ460 and XZ499, which strafed the vessel with 30 mm cannon fire.

The Argentine Naval Prefecture purchased five Short SC.7 Skyvan unarmed light transport aircraft in 1971, which they gave the call signs PA-50 to PA-54.

The Prefecture is constantly battling illegal fishing vessels in the Argentine exclusive economic zone (EEZ),[4] mostly from eastern countries.

The Taiwanese fishermen's union called the incident a "barbaric act" and the British government condemned it as "unjustifiable and excessive".

The Prefecture's main facility is located in the Edificio Guardacostas (which translates as "the Coastguard Building") at 235 E. Madero Avenue, Buenos Aires.

[13] Previous fixed-wing types include Grumman G-21 Goose (6), de havilland DH.104 Dove (2), Nord 1203 Norécrin (4), Douglas C-47 (2), Short SC.7 Skyvan (5)[15]