Trapped organic compounds (lipids) have been analysed in tubular carbonate concretions and their host sediments in Miocene deep water mudrocks from coastal outcrops in East Coast Basin and Taranaki Basin of North Island, New Zealand. The concretions, including calcitic, dolomitic and mixed mineralogies, have varied morphologies in many cases suggestive of conduits or pipes that channelled the escape of subsurface fluids and/or hydrocarbon gases. The extracted lipids include water column and/or diagenetically-derived alkanes, fatty acids and alcohols as well as specific marker compounds (including archaeal pentamethylicosane (PMI) and archaeol) associated with subsurface anaerobic oxidation of upwardly seeping methane gas (AOM). Strong carbon-13 isotopic depletions (δ13C –75 to –120‰) measured for PMI, archaeol and other AOM-specific marker compounds on three concretion samples support involvement of AOM in generating bicarbonate-rich fluid that was at least partly responsible for cementing the pipe-like concretions and central conduits. Other morphological types appear not to be AOM-related. Sterane and n-alkane parameters indicate low thermal maturity of the extracted organic matter. The molecular and compound specific isotopic organic geochemical evidence that some tubular concretions functioned as methane conduits thus supports an assertion that the tubular concretions represent 'fossilised' parts of the subsurface plumbing of biogenic or thermogenic hydrocarbon-fed cold seep systems.