The spin transport properties of a series of 3d transition metal(II) phthalocyanines (MPc, M = Mn, Fe, Co, Ni, Cu and Zn) sandwiched between two semi-infinite armchair single-walled carbon nanotube electrodes are investigated by using a self-consistent ab initio approach that combines the non-equilibrium Green's function formalism with spin density functional theory. Our calculations show that among the six molecules only MnPc and FePc can act as nearly perfect spin filters and at the same time have a large transmission around the Fermi level. This is dominated by the highest occupied molecular orbital (HOMO) of the corresponding MPc molecule. In contrast to the other four MPc molecules, whose HOMO is the a1u orbital located over the Pc ring, the HOMO of MnPc and FePc is a doubly degenerate π-type orbital composed of the 3dxz and 3dyz atomic orbitals of the metal center. The spin polarization of MnPc and FePc is independent of the size of the SWCNT electrodes and can be tuned by chemisorption at the metal center, demonstrating that MPc and carbon nanotubes are a promising materials platform for applications in molecular spintronics.