Tens of thousands of households experienced power cuts and almost 150 flights to and from Okinawa were grounded on Friday.
Weather forecasters predict the storm which was headed northward will hit western Japan on Saturday.
The storm is the fourth typhoon this season.
The Meteorological Agency said Man-Yi clocked sustained wind speeds of up to 180 kilometres per hour as it slammed into Naha, the prefectural capital of Okinawa.
Tomoko Sunagawa, an official of Okinawa Electric Power Co, said about 60,000 households, or 11 per cent of all households in Okinawa, were without power.
It was not immediately clear when power would be restored.
More than 300 flights in and out of Okinawa and Kyushu were also cancelled, according to Kyodo news agency.
Japan Airlines grounded 59 flights while All Nippon Airlines cancelled 110.
On Tuesday, a Chinese vessel capsized 600 kilometers northwest of Guam in rough seas due to Typhoon Man-Yi, China's state news agency Xinhua reported.
Ten people were rescued on Wednesday but a dozen crew members were still missing, officials at the Chinese consulate in Los Angeles were quoted as saying.