Plans to convert a defence site into a freight hub in Sydney's south-west can proceed, provided developers implement strict conditions to protect a rare flowering plant, the Land and Environment Court has decided.

The discovery of 370 individual Hibbertia fumana plants - a species last documented in 1823 and long thought extinct - threatened to stall development of the $1 billion-plus Moorebank Intermodal Terminal Facility.

The court imposed conditions on the project, which will be finalised in about a week. According to the earlier agreed conditions, Qube, the developer, will be required to develop a Hibbertia species survey plan to assess the number of individual plants within the rail corridor.

A disused rail spur traversing the Southern Boot Land must also be removed and remediated.

Once rehabilitation is complete, the developers are to the seek Office of Environment and Heritage approval to include sections of the remediated land as part of a biobanking agreement, according to the earlier conditions.