Judging from what is seen in the episode "Durka Returns", the craft is, at its smallest, 40 to 60 meters long, with a step-sectioned cylindrical body that grows out of a spheroid/egg-like rear drive system, and 3 pylons, implied to be maneuvering thruster assemblies, arranged in a triangle pattern when viewed from the front. the pylons are attached to the craft on some sort of gymbal structure, at the junction of the main body and the drive section.
the front of the craft is mostly flat, with a main viewing port that is not unlike a (tie fighter/Millenium Falcon) viewport.
While size continuity is rather troublesome, it is logical to presume that the Nebari Transport is meant to wander about away from a host vessel for a time, though not indefinetly. Assuming this fact, it is logical to presume that there is room for a cockpit, 4 prisoner cells, 1 crew barracks room with 4 bunks, an engineering room or closet, a refresher room, and perhaps a cargo room or storage lockers.
Defenses and Armaments
The transport possesses an energy weapon which Durka referred to as a "phase cannon."