Like all Podocarpus species, Podocarpus nakaii is dioecious, bearing male and female cones on the same tree (2). The male cones, which measure up to five centimetres in length, grow individually or in clusters of two to three at the bases of leaves, and are covered in small scales (2) (3). The female cone grows on a short stalk, and is highly modified, becoming swollen, fleshy and berry-like at the base. Measuring up to 1.2 centimetres long, the base is composed of two lobes, separated by grooves, and becomes red at maturity. Each cone bears a single, plump, unwinged seed (2) (3) (4). The female cones of Podocarpus nakaii usually ripen by April (4), maturing and falling within a single season (2).
Interestingly, Podocarpus nakaii has been shown to produce chemicals which mimic certain insect moulting hormones. These chemicals are believed to disrupt the growth and development of insects that ingest them (5) (6) (7), and may serve to protect the tree against insect attack (7).