Temporal information-processing is critical for adaptive behavior and goal-directed action. It is thus crucial to understand how the temporal distance between behaviorally relevant events is encoded to guide behavior. However, research on temporal representations has yielded mixed findings as to whether organisms utilize relative versus absolute judgments of time intervals. To address this fundamental question about the timing mechanism, we tested mice in a duration discrimination procedure in which they learned to correctly categorize tones of different durations as short or long. After being trained on a pair of target intervals the mice transferred to conditions in which cue durations and corresponding response locations were systematically manipulated. Specifically, responses and/or durations of cues were switched in different experimental phases so that either the relative or absolute mapping remained constant. The findings indicate that the transfer occurred most readily when relative relationships of durations and response locations were preserved. In contrast, when the animals had to re-map these relative relations, their temporal discrimination ability was impaired, and they required extensive training to re-establish temporal control. However, preserving the response location of one of the cue durations in such conditions was found to help with initial transfer. These results demonstrate that mice can represent experienced durations both as having a certain magnitude (absolute representation) and as being shorter or longer of the two durations (an ordinal relation to other cue durations), with relational control having a greater influence in temporal discriminations.