A plant propagation system and method are provided for promoting the growth of plant tissue into small plantlets. The plant propagation system includes sealed, semipermeable membrane vessels for completely enclosing plant material therein. The sealed vessels generally are translucent and permeable to gases and liquids while remaining impermeable to biological contaminates. Plant tissue originally extracted from a parent plant can be placed within the sealed vessels and grown heterotrophically. Once the plant material has developed the capability to photosynthesize, the sealed vessels can be transferred to a greenhouse environment for photoautotrophic growth. Once in a greenhouse environment, the sealed vessels are supported in trays and exposed to light, gases, water and a liquid nutrient solution for optimizing growth. A central controller can be included in order to automate the system for controlling the flow of fluids in and out of the vessel support trays while also monitoring system conditions. A disinfectant can also be circulated within the system for destroying biological contaminants in the tray and outside the sealed vessels for maintaining an aseptic environment.