The royal couple, who married on 21 September, visited the museum's gardens and carp pond and took tea with the museum's deputy director, Ms. Hiroko Nishida, on the veranda of one of the houses in the garden.
Princess Claire, née Claire Lademacher, sported an all-black ensemble of a dress, blazer and clutch bag and added a pop of colour with a blue beaded necklace and cornflower loafers.
Félix and Claire are currently visiting Japan to celebrate Sophia University's 100th anniversariy on behalf of Grand Duke Henri and Grand Duchess Maria Teresa.
Earlier in their visit the duo attended a mass held at St Ignatius Church and met Luxembourgish nationals living in Japan during a reception held in their honour at the Grand Duchy's embassy.
The couple married in a romantic ceremony surrounded by their family and friends.
The pair said "I do" in Saint-Maximin-la-Sainte-Baume's magnificent 13th century Sainte Marie-Madeleine basilica.
The bride wore a stunning floral-detailed long-sleeved gown by Elie Saab, the Luxembourg royal family's go-to designer.
Guests included Monaco's Pierre Casiraghi and his girlfriend Beatrice Borromeo, and members of the Luxembourg's Grand Ducal family, including Prince Guillaume and Princess Stephanie and the Lademacher family.