TOKYO—A powerful earthquake shook central Tokyo on Monday afternoon, causing temporary suspension of the area’s train system and the runways at one of the capital’s airports.

The magnitude 5.5 quake—centered on the northern part of Saitama prefecture, northwest of Tokyo, and 56 kilometers (35 miles) below ground—struck at 2:28 p.m. local time (0528 GMT), according to the Japan Meteorological Agency.

It...