After Angamos, Peru’s Navy was left only with the two old Canonicus monitors, the wooden corvettes Union and Pilcomayo, the gunboat Arno and some torpedo boats. None of those ships however could match the strong Chilean battleships, although they gave invaluable support in delivering necessary equipment to the Peruvian garrisons in the South by breaking the dangerous blockades imposed by the Chileans.
For all effects the war at sea had almost concluded. In November 1879, the small corvette Pilcomayo was captured in combat by the battleship Blanco Encalada. On December 22 the torpedo boat Alay suffered the same fate. On June 7, 1880, after the battle of Arica, the monitor Manco Capac was scuttle by her crew. Although there would be no longer naval actions of importance, some particular engagements demonstrated the determination of the Peruvian naval officers to continue the struggle in spite of their disadvantage.
Past midnight, May 25, 1880, the modern Chilean Spar torpedo boats Guacolda and Janaqueo, armed each with two torpedo tubes, one small gun and one machinegun, discovered three Peruvian gunboats on their way to Callao and tried to stop them. The fast Janaqueo, under Lieutenant Manuel Señoret, approached the Independencia, under Lieutenant Jose Galvez -who was the son of the hero of the 1866 “2 de Mayo” combat- and fired a torpedo that almost destroyed the Peruvian boat and killed eight of her crew of thirteen. Nevertheless, Galvez injured as he was, charged with his crippled ship against the opponent and by hand and under heavy fire, with the help of another brave officer, Manuel Ugarte y Moscoso, he threw a 50-kilogram torpedo inside the Janaqueo. The explosion killed two enemy sailors and destroyed their boat. The Chileans were so impressed by Galvez courage, that few hours after he was taken prisoner to the battleship Blanco Encalada, he was returned to the Peruvian authorities in Callao. Ugarte y Moscoso died in the action.
Later, on December 6 of that year, a second torpedo-boat combat took place. The Peruvian gunboat Arno, armed with two guns, and the torpedo boats Capitania, Resguardo, Urcos and Republica, fought against the Chilean torpedo boats Fresia, Guacolda, Colo Colo and Tucapel, armed each with two torpedoes and one Hotchkiss machinegun. As a result of the combat, the gunboat Arno sunk the 25-ton torpedo boat Fresia, under command of Lieutenant Alvaro Bianchi.
The Peruvians also sink the 1,657-ton steamer Loa, one of the ships that participated in the final hunt of the Huascar. The ship was destroyed off Callao on July 3, 1880, by an explosive charge hidden by the Peruvians inside a boat, which Loa’s Commander, Juan Peña, imprudently order to pick up at sea. The commander and 119 crewmen died during the terrible explosion.
On September 13th, 1880, off the coasts of Chancay, North of Lima, the old schooner Virgen de Covadonga, which also fought against Huascar in Angamos, suffered identical fate that the Loa. Her commander, Pablo Ferrari, imprudently decided to hoist up what was supposed to be a harmless small vessel. The boat was loaded with explosives. The terrible explosion sent the schooner to the bottom of the sea in a matter of minutes. From her crew of 109 men, 32, including the Captain, died during the explosion, while 29 escaped in boats and 48 become prisoners of war of the Peruvian army
On January 3, 1881, however, the Chilean corvette O´Higgins would sink the torpedo boat Republica after she tried to execute a night raid against the Chilean ironclads off Callao.
Few days later, after the battle for Lima, to avoid the fleet falling into enemy hands, the Government ordered to destroy the remaining ships of the armada: The corvette Union, the monitor Atahualpa, the gunboat Arno, the torpedo boats, the submarine and all the transports.
With those actions, the Peruvian Navy would cease to exist temporarily, until her rebirth took place at the end of the decade, with the arrival of the gunboat Lima.