When the Second Schleswig War broke out, Hammer enlisted again as an officer and lead a flotilla in the North Frisian Islands.

Retiring again from military duties, Hammer became involved in politics and established a lumber and fishery business in Sweden.

On an expedition to qualm uprisings in the Danish colonies in Guinea in 1854, he led the expeditionary forces to Fort Prinsensten and negotiated with the locals.

His forces occupied the islands Nordstrand and Pellworm and Hammer took part in the defense of the then Danish towns of Tönning and Friedrichstadt.

[2] At the onset of the Second Schleswig War, Hammer enlisted again and commanded a flotilla of Danish naval units in the North Frisian Islands with his headquarters in Wyk auf Föhr.

But when requested reinforcements did not arrive and his opponents were able to capture the island of Sylt and then Föhr, Hammer himself was taken prisoner by Prussian Lieutenant Ernst von Prittwitz und Gaffron on 19 July 1864 in Wyk, and was held captive until August of that year.

Hammer published a book on his experiences in the war of 1864: In 1872, he was awarded a gold medal by the Moscow Scientific Society for a treatise on fishery matters.