The magnetic structure of quasi-two-dimensional (2D) honeycomb lattice Na2Ni2TeO6 has been determined by low-temperature neutron diffraction and the crystal structure fine details at room temperature have been established by a combination of synchrotron and neutron powder diffraction. The atomic structure is described by the P63/mcm space group, but the strong presence of stacking faults defects in layered ordering is found for the first time. Both magnetization and specific heat data indicates an establishment of a long-range antiferromagnetic order with TN = 251 K, preceded by a short-range order on 2D honeycomb lattice at about 34 K. Determined effective magnetic moment μeff = 4.35 μB is in excellent agreement with numerical estimation using effective g-factor g = 2.19 directly measured by electron spin resonance. The ground magnetic state at T = 1.5 K is represented by the commensurate zigzag-type magnetic order. Magnetic moments of Ni are almost perpendicular to the honeycomb layers, which antiferromagnetically coupled along the c-direction. Besides, the coherent magnetic scattering area has a disk shape that is homogeneous over the ab plane and compressed along the c-axis that indicates 2D nature of magnetic correlations in the compound. The magnetic diffuse neutron scattering related to the presence of strong short-range spin-spin correlations above TN was observed. Based on our experimental measurements we propose magnetic phase diagram for Na2Ni2TeO6.