Japan it should be remembered started from a much higher base line.

The Washington and London Naval treaties fixed the proportions if the great powers fleets.

For the US/UK and Japan the ratio was 5/5/3 for tonnage and number of ships essentially.

This had major support amongst some in the IJN. They knew that the US could outbuild Japan to a hilarious degree, thus artificially fixing them to only a bit more than Japan was a win. Yamamoto was a vocal member of this faction. Essentially then all 3 fleets were more or less complete by 1930, with just the cruisers and carriers being built. Then Japan revoked the treaties and began building again but completed only a relative gaggle of ships before the start of the war.

Germany meanwhile started from almost nothing. The High Seas Fleet was interned and scuttled itself at Scapa Flow in 1919. Then most remaining ships were distributed as war prizes. She retained only a few cruisers and pre dreadnoughts for most of a decade. And only began serious construction in the Mid 30s. And even then the much more diverse nature of the German arms industry and defense needs meant a very small percentage if resources went towards surface ship construction compared to Japan.

Another thing is that Japan could not make up for the much greater shipbuilding capacity of the U.S. The U.S. had far more shipyards than Japan, and despite all the territory Japan was able to conquer at the start of the war there were no shipyards capable of building anything larger than a destroyer in all of the occupied territory.

So Japan's shipbuilding was largely fixed, and the U.S. capacity was much larger and also underused in the pre-war years. After Pearl Harbor, U.S. shipyards started building almost 100 'jeep' carriers, and eventually ended with dozens of larger fleet carriers, while Japan was only able to add 3 carriers to its fleet. Japan could simply not keep up with either the U.S. building, or its own losses.

Source: Shattered Sword