The first complete submillimetre spectrum ( 190-670 \mu m ) of the Seyfert 2 galaxy NGC 1068 has been observed with the SPIRE Fourier Transform Spectrometer onboard the Herschel Space Observatory . The sequence of CO lines ( J _ { up } =4-13 ) , lines from H _ { 2 } O , the fundamental rotational transition of HF , two o-H _ { 2 } O ^ { + } lines and one line each from CH ^ { + } and OH ^ { + } have been detected , together with the two [ CI ] lines and the [ NII ] 205 \mu m 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 _ { kin } =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 } ) \sim 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 Herschel 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 } ) . The emission of H _ { 2 } O ^ { + } and OH ^ { + } are in agreement with PDR models with cosmic ray ionization . The diffuse ionized atomic component observed through the [ NII ] 205 \mu m line is consistent with previous photoionization models of the starburst .