The president will also attend a banquet to be hosted by the Japanese prime minister
The ceremony took place at the State Hall of Imperial Palace at 1pm (local time) on Tuesday, reports UNB.
The enthronement ceremony was held as a part of national ceremony (from Oct 22 to October 31) to celebrate the enthronement of the emperor.
First Lady Rashida Khanam, and Bangladesh Ambassador to Japan Rabab Fatima also accompanied the president at the program.
Tuesday's Sokuirei no Gi (enthronement ceremony) is considered to be the most important of a series of enthronement- related ceremonies that started in May.
The ceremony at the Seiden State Hall started at 1pm in Matsu no Ma state room, with the Emperor announcing his enthronement from the 6.5-meter-high canopied throne, known as the takami-kura.
President Hamid reached Tokyo on Monday on an eight-day official visit to Japan and Singapore.
Some 2,000 people, including heads of states and other dignitaries, from 174 countries attended the enthronement ceremony.
The president is scheduled to visit Yokohama, Japan’s second largest city, on Wednesday.
Kosovo President HashimThaçi will meet Abdul Hamid at Hotel New Otani in Tokyo on the same day.
The Bangladesh president will also attend a banquet to be hosted by Japanese Prime Minister Shinzo Abe at Hotel New Otani on the same day, as part of the ceremony.
President Hamid will visit Singapore from October 25-27 on his way back home.
He is expected to return home on October 27.