It is an object of the invention to provide a method and an apparatus for processing a very large number of fish eggs for gene injection and so on with a superior performance. An egg case has an egg-arranging plate and a cover plate. The fish eggs are dropped into concave portions of the egg-arranging plate, when the cover plate opens the concave portions. The cover plates closes the concave portions after fish eggs are accommodated in the concave portions.The egg case is fixed on a table of an egg-arranging apparatus. water is supplied on the egg-arranging plate in the egg plate. A scanning nozzle sprays water on upper surface of the egg-arranging plate. After closing the concave portions with the cover plate, the egg case is inclined for dropping fish eggs remaining on the cover plate.