Zebrafish lateral-line hair cells are an in vivo model for studying hair cell development, function, and ototoxicity. However, molecular identification and properties of the mechanotransducer (MET) channel in hair cells are still controversial. In this study, a noninvasive electrophysiological technique, the scanning ion-electrode technique (SIET), was applied for the first time to investigate properties of MET channels in intact zebrafish embryos. Using a Ca²⁺-selective microelectrode to deflect hair bundles and simultaneously record the Ca²⁺ flux, the inward Ca²⁺ flux was detected at stereocilia of hair cells in 2~4-days post-fertilization embryos. The Ca²⁺ influx was blocked by MET channel blockers (BAPTA, La³⁺, Gd³⁺ and curare). In addition, 10 µM aminoglycoside antibiotics (neomycin and gentamicin) were found to effectively block the Ca²⁺ influx within 10 min. Elevating the external Ca²⁺ level (0.2 to 2 mM) neutralized the effects of neomycin and gentamicin. However, elevating the Mg²⁺ level up to 5 mM neutralized the blockade of gentamicin but not neomycin. This study demonstrated MET channel-mediated Ca²⁺ entry at hair cells and showed the SIET to be a sensitive approach for functionally assaying the MET channel in zebrafish.