The calcareous contourites from the Late Oligocene and Early Miocene in the Petra Tou Romiou type section (southern Cyprus) have been studied in detail, being regarded as outstanding examples of fossil bioclastic contourites and representative of the standard facies model of contourite bigradational sequence. These bigradational sequences of sand-dominated contourites consists of whitish calcarenite beds with wavy layering in the middle portion of the sequence. Gradual alternations of whitish and greenish calcilutites appear above and below these calcarenites. The internal wavy layering is composed by compacted interlayers and non-compacted interstratified layers. In the present study, an in-depth ichnological analysis of the bigradational sequence has been conducted, focusing on ichnological features such as length, shape, diameter, and orientation of individual burrow segments, the configuration of burrow systems, as well as external features, fill material, and finally taphonomy. Trace-fossil assemblages differ, containing Planolites isp., Chondrites isp., and ?Thalassinoides isp. at the compacted interlayers, and non-compacted layers bearing only Planolites structures. The compacted interlayer structures are flattened and elliptical, containing similar fill material as the calcilutite host sediment, though lighter in color. In the non-compacted layers, Planolites are near un-deformed, being cylindrical and tubular, with circular to sub-circular cross-sections. These are located mainly at the base or occupy the entire layer, locally showing longitudinal striae (Planolites reinecki Książiewicz), and filled with calcarenite material. The different trace-fossil assemblages in the compacted layers and non-compacted interlayers, varying in fill material, evidence an original primary differentiation, presumably indicative of fluctuating paleoenvironmental conditions. In consecutive non-compacted layers, the distribution of Planolites is separated by compacted interlayers. This indicates that the middle portion of the contourite type facies, with internal wavy layering, underwent a multiphase deposition. In the non-compacted layers, the almost undeformed Planolites, marked by striae, is consistent with a higher substrate consistency, which is interpreted as being associated with sedimentary condensation or omission, immediately before the next compacted interlayers were deposited. This evidence clearly supports the contention that sedimentary processes governing contourite deposition were intermittent rather than continuous, as traditionally proposed. These findings raise basic questions regarding the bottom current processes, and consequent bedform development in these deep-marine environments.