With the retirement of admiral Ulrich Anton Schønheyder from the admiralty college in 1846, Schifter took over as a deputy head – a post he served for two years. He was newly advanced to second in command of the navy but left shortly afterwards to become chief of the naval dockyards ("overekvipagemester" ). In this position he found himself leading the naval mobilisation for the war of 1848 -50 (Schleswig Holstein Question) which involved much of the fleet that he had built.