Several approaches for immobilization of arsenic (As) based on the transformation of its soluble forms (compounds) into highly insoluble arsenate apatite Ca5(AsO4)3OH have been proposed. These immobilization techniques are successfully applied in treatment of industrial waste containing As. Quite the contrary, treatment of soil contaminated with As by apatite amendments, instead of immobilization of this toxic element, increases its mobility and bioavailability. The mechanism underlying these opposite effects still remains elusive. Here, the stability analysis of different calcium arsenates: Ca5(AsO4)3OH, Ca4(AsO4)2(OH)2, Ca3(AsO4)2 Ca5H2(AsO4)2 and CaHAsO4 was performed, which is based on the calculation of the ion-ion interaction potential (IIIP). It has been demonstrated earlier that IIIP, representing the main term of the cohesive energy, is a suitable parameter for assessment of mineral stability. According to the results of this analysis, arsenate apatite with IIIP value of -0.578 Ry represents the most stable chemical form among analyzed compounds. Based on this finding, we proposed a mechanism of formation of arsenate apatite in the presence of hydroxyapatite. This mechanism can explain the suitability of this approach for the treatment of industrial waste and its limitations for in situ treatment of soil and water contaminated with As.