The estimation of planetary magnetic fields from observations of the magnetic field gathered along a spacecraft flyby trajectory is examined with the aid of generalized inverse techniques, with application to the internal magnetic field of Jupiter. Model non-uniqueness resulting from the limited spatial extent of the observations and noise on the data is explored and quantitative estimates of the model parameter resolution are found. The presence of a substantial magnetic field of external origin due to the currents flowing in the Jovian magnetodisc is found to be an important source of error in estimates of the internal Jovian field, and new models explicitly incorporating these currents are proposed. New internal field models are derived using the vector helium magnetometer observations and the high field fluxgate observations of Pioneer 11, and knowledge of the external current system gained from the Pioneer 10 and Voyagers 1 and 2 encounters.