Flowering occurs unpredictably throughout the year and is followed by fruit which are woody capsules 2.5–4 mm (0.1–0.2 in) long, arranged in cylindrical spikes.

[2][3] The species was first formally described in 1968 by Stanley Thatcher Blake from a specimen collected north-west of Cooktown and west of Cape Bedford in Three Islands National Park.

The specific epithet (arcana) is from the Latin arcanus, meaning "secret" or "mysterious" in reference to the species' apparent rarity.

[2] Melaleuca incana occurs on the east coast of Cape York Peninsula in the swales between sand dunes.

[6] In some situations this species may be preferable to Melaleuca leucadendron as a street tree because of its smaller size at maturity.