We demonstrate a water-based etching strategy for converting solid silica shells into porous ones with controllable permeability. It overcomes the challenges of the alkaline-based surface-protected etching process that we previously developed for the production of porous and hollow silica nanostructures. Mild etching around the boiling point of water partially breaks the imperfectly condensed silica network and forms soluble monosilicic acid, eventually producing mesoscale pores in the silica structures. With the surface protection from poly(vinyl pyrrolidone) (PVP), it is possible to maintain the overall shape of the silica structures while at the same time to create porosity inside. By using bulky PVP molecules which only protect the near-surface region, we are able to completely remove the interior silica and produce hollow particles. Because the etching is mild and controllable, this process is particularly useful for treating small silica particles or core-shell particles with very thin silica shells for which the alkaline-based etching method has been difficult to control. We demonstrated the precise control of the permeation of the chemical species through the porous silica shells by using a model reaction which involves the etching of Ag encapsulated inside Ag@SiO(2) by a halocarbon. It is expected that the water-based surface-protected etching method can be conveniently extended to the production of various porous silica shells containing functional materials whose diffusion to outside and/or reaction with outside species can be easily controlled.