The features of the crystal structure and spin order in the ground state of two samples of layered honeycomb oxides of the same stoichiometric composition Li2Ni2TeO6 were established by the neutron powder diffraction method. These samples were synthesized by the ion-exchange method from different precursors, Na2Ni2TeO6 and K2Ni2TeO6, having a similar crystal structure, hexagonal space group P63/mcm, but with a significant difference in the distances between the layers. Both Li2Ni2TeO6 samples do not retain the structure of the precursors and crystallize into the orthorhombic space group Cmca, with very minor differences in the unit cell parameters. While Li2Ni2TeO6 from the potassium precursor is single-phase, the sample from the sodium precursor appears to be a mixture of two crystal modifications. Its main phase is crystallized in Cmca, and the second phase, 13.6 wt.%, with the same Li2Ni2TeO6 stoichiometry, is more deformed, with monoclinic distortions described by the C2/m space group. The values of the fragments of the fine crystal structure have been calculated. The coherent coupling of the two phases at the unit cell level was shown. The magnetic structures of the investigated samples in the ordered magnetic state at T = 1.5 K have been determined and described in detail. A relatively small incommensurability of the magnetic structure is manifested across all three crystallographic directions. The magnetic propagation vector can be represented as k = (1/2-δ1, 1/2-δ2, 1/2-δ3) at small values of δ, i.e. the magnetic unit cell is almost doubled in relation to the crystallographic one. The magnetic order is three-dimensional and represents an antiferromagnetic ordering of magnetic Ni ions in honeycomb ab planes of the stripe type with magnetic moments coming out of the honeycomb plane. The influence of the presence of a mixture of phases of stoichiometric composition but different crystal structure on the magnetic ordering of Li2Ni2TeO6 has been studied.