Diagnoses in patients with disorders of consciousness are prone to misdiagnosis; thus, research has sought approaches to increase reliability, for instance, with functional MRI. By applying a motor imagery task, patients showing covert command following despite the absence of behavioural signs of awareness can be identified as being in a cognitive motor dissociation. This study seeks to determine the proportion of patients, with unresponsive wakefulness syndrome and minimally conscious state, who display covert command following. Moreover, the prognostic value of the improved diagnosis and different methodical approaches to analyse the functional MRI data were evaluated. 73 disorder of consciousness patients (35 unresponsive, 35 minimally conscious, and three already recovered) underwent weekly standardized behavioural assessments with the coma-recovery scale—revised and one functional MRI examination comparing their brain activations in the supplementary motor area between phases of imaging playing tennis and rest. 27 healthy controls served as a control group. The data was evaluated using different region-of-interest analyses (one- and two-tailed small-volume correction and region-of-interest exploration approaches) and a whole-brain analysis. Based on the one-tailed small volume correction data, seven patients, all of nontraumatic aetiology, showed covert command following. The one-tailed region-of-interest exploration identified three additional responders. 10 patients showed significantly more activation during rest than during the imagery paradigm (negative responders). 40% of patients (minimally conscious patients being three times more likely) showed significant activations in the whole brain analysis. Besides, no significant further associations were found between covert command following and clinical parameters. The analyses showed that the tennis paradigm could identify patients with cognitive motor dissociation with a nontraumatic aetiology, but our data failed to show any short-term prognostic validity. The relevance of negative responders and activated regions outside of the region of interest should be further investigated.