Ru-containing catalysts based on aluminosilicate halloysite nanotubes (HNTs) are synthesized by preliminary functionalization of the support surface by aminopropyltriethoxysilane (APTES) followed by the microwave-assisted deposition of ruthenium to provide the intercalation of metal nanoparticles into the inner space of nanotubes. The composition and structure of the synthesized catalysts are studied by X-ray fluorescent analysis, low-temperature nitrogen adsorption/desorption, transmission electron microscopy, and hydrogen temperature-programmed reduction. The activity of the catalysts in benzene hydrogenation at a temperature of 80 degrees C and a hydrogen pressure of 3 MPa both in the hydrocarbon medium and in the two-phase system with water is studied. It is shown that, in the presence of water, the hydrogenating activity of the catalyst based on modified halloysite nanotubes is considerably higher than that of the sample prepared using the initial halloysite as a support.