Anomalous modulation characteristics of Josephson current $I_{c}$ through a niobium tunnel junction have been measured by applying the external magnetic field in perpendicular direction. Josephson current $I_{c}$ through a superconducting niobium/aluminum-oxide/niobium tunnel junction is modulated by applying the parallel magnetic field $(H_{x},H_{y})$ and the vertical field $H_{z}$ to the junction plane using three pairs of Helmholtz coils. Modulation characteristics of the $I_{c}$ value upon the vertical field $H_{z}$ have hysteresis. Before applying the vertical field $H_{z}$ , the $I_{c}-(H_{x},H_{y})$ dependences are the product of the two Fraunhofer diffraction patterns in the $H_{x}$ and $H_{y}$ directions parallel to each edge of the square-shaped junction and show a square-shaped main peak area. After applying the vertical field $H_{z}$ more than 5000 A/m, during the removing process of this vertical field $H_{z}$ , the $I_{c}-(H_{x},H_{y})$ modulation pattern shows a triangle-shaped main peak area due to the remained trapping and shielding magnetic flux at niobium electrodes.