The first complete submillimetre spectrum (190-670um) of the Seyfert 2 galaxy NGC1068 has been observed with the SPIRE Fourier Transform Spectrometer onboard the {it Herschel} Space Observatory. The sequence of CO lines (Jup=4-13), lines from water, the fundamental rotational transition of HF, two o-H_2O+ lines and one line each from CH+ and OH+ have been detected, together with the two [CI] lines and the [NII]205um line. The observations in both single pointing mode with sparse image sampling and in mapping mode with full image sampling allow us to disentangle two molecular emission components, one due to the compact circum-nuclear disk (CND) and one from the extended region encompassing the star forming ring (SF-ring). Radiative transfer models show that the two CO components are characterized by density of n(H_2)=10^4.5 and 10^2.9 cm^-3 and temperature of T=100K and 127K, respectively. The comparison of the CO line intensities with photodissociation region (PDR) and X-ray dominated region (XDR) models, together with other observational constraints, such as the observed CO surface brightness and the radiation field, indicate that the best explanation for the CO excitation of the CND is an XDR with density of n(H_2) 10^4 cm^-3 and X-ray flux of 9 erg s^-1 cm^-2, consistent with illumination by the active galactic nucleus, while the CO lines in the SF-ring are better modeled by a PDR. The detected water transitions, together with those observed with the her sim PACS Spectrometer, can be modeled by an LVG model with low temperature (T_kin sim 40K) and high density (n(H_2) in the range 10^6.7-10^7.9 cm^-3).
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