Prime Minister Shinzo Abe is scheduled to hold a news conference at 6pm (0900 GMT) when he is expected to announce the lifting of the emergency in 39 of Japan's 47 prefectures, but not in Tokyo.
Pope Francis called on Monday for renewed efforts to help victims of Japan’s 2011 “triple disaster” of earthquake, tsunami and the Fukushima meltdown, noting “concern”
On wasteland once used for earthquake drills in the small town of Otawara north of Tokyo, Japanese giant Shiseido has built its first domestic factory in 36 years, hoping to capitalise on a boom for "Made in Japan" cosmetics.
Nintendo this week throws open the doors to its first bricks-and-mortar store in Tokyo, offering everything from Super Mario mugs to Zelda handbags as part of a new gaming complex in the heart of the city.
The Nikkei 225 index rose 1.33 percent, or 293.10 points, to close at 22,288.14 while the broader Topix index was up 0.62 percent, or 9.55 points, at 1,558.77.
Visitors in face masks queuing on floor marks clapped as the gates of the Magic Kingdom reopened and were encouraged to clean hands, pay without cash and avoid screaming while enjoying one of Japan's largest theme parks.
The benchmark Nikkei 225 index rose 0.72 percent, or 160.52 points, to 22,306.48. It lost 0.91 percent over the week.
Retailers in Japan began charging for plastic bags on Wednesday, a move aimed at curbing Japanese consumers' love for packaging and finally bringing the country in line with other major economies.
The Nikkei 225 fell 1.22 percent, or 274.53 points, to close at 22,259.79 while the broader Topix index was down 1.18 percent, or 18.65 points, at 1,561.85.