The agency has also warned of high winds, gales and flooding across central and southern Japan.
"Rain will be very heavy and winds will also be fairly strong on land. It is likely to make landfall with a violent force," the agency said.
In some parts of Tokyo, local authorities have made sandbags available to residents who wanted to protect their homes against flooding from rivers and canals.
People living in the expected path of the storm have been told to put shields on windows, fill their bathtubs in case of cuts in the water supply, and to gather daily necessities for a possible evacuation.
According to some projections, Melor could follow a course similar to Typhoon Vera in 1959 which tore through Honshu, causing widespread flooding and leaving more than 5,000 dead and tens of thousands homeless in one of Japan's worst natural disasters.