Prosecutors are examining whether the Swedish Fortifications Agency neglected its duties when it failed to detect the arrival at the Muskö base of the populous school of minnows.
Among the tasks assigned to the agency, which is one of the largest landowners in Sweden, is responsibility for the upkeep of secure underground military facilities around the country.
Property manager Christer B. Andersson said the agency was taken completely by surprise by the enormous quantities of fish left behind when the dock's gates were opened.
"We emptied other docks as recently as a few weeks before emptying this dock and only came across the occasional fish. It's a bit of a mystery actually," he told Sveriges Radio.
"Roach move in a very strange manner and they often move about in large schools. If we're unlucky, a very large school might have got into this slipway and been left behind when we closed the outermost gates in order to be able to empty the water," he added.
Andersson said the agency had taken steps to ensure that all docks would in future be checked for fish before emptying.