The Kairei and Yokoniwa hydrothermal fields are hosted in mafic as well as ultramafic rocks distributed at an off-axis volcanic knoll of the Central Indian Ridge. Despite intensive investigations, their geological and geophysical background is still debated. Here, we show results of near-seafloor magnetic field measurements using a submersible. We investigated crustal magnetization of the hydrothermally altered zone and surrounding lava flows, and evaluated their intensities compared to previously reported values at axial areas of a spreading environment. The Kairei hydrothermal field is characterized by low coherence between observed and modeled anomalies and low values of magnetization. This result suggests that magnetic minerals within basaltic lava flows were likely altered by hydrothermal fluid circulation. The variation pattern in the observed magnetic anomalies above the lava flows is in phase with that of modeled magnetic anomalies for a simple assumption with a magnetization direction parallel to the geomagnetic field. This result suggests that these lava flows preserve normal magnetic polarity corresponding to the Brunhes chron. The estimated magnetization intensity reaches 20 A/m in this area, which is clearly greater than that of the general off-axis crustal magnetization. This study provides new insight into the distribution of highly magnetized lava flows and indicates the distribution of recent off-axis volcanic activity, which is potentially linked to sub-seafloor hydrothermal circulation.