The flowers of Habenaria epipactidea are densely clustered in a spike of green and creamy white. The sepals are inconspicuous and pale green. The lateral petals, conspicuous at the top of the flower, are broad, in picture nearly square and white, cream or greenish white in colour with green veins on their surfaces. The petals of this species are unlobed with the top inside corners sometimes slightly elongated and curving inwards.
The lip at the bottom of each flower is white and narrowly tongue-shaped. It has a pair of tiny, thin whisker-like lobes at its base, pointing sideways and angled downwards. The spur that grows from the lip is club-shaped, greener towards the tip and whiter near the base. The spur points backwards, angled or curved downwards about halfway along its length. It may reach 6 cm in length.
The stigmas are two slender stalks not joined to the lip. There is a flat rostellum lobe above, extending from the stigma and separating the stamen from the female parts (Manning, 2009; Lowrey and Wright, 1987).