The china cup and saucer set was used by the star at a press conference in Tokyo three months after the massive tsunami of March last year swamped a large stretch of coastline.
Lady Gaga told reporters at the time that she would auction the cup, marked with her lipstick and bearing the Japanese message "We pray for Japan" along with the star's autograph.
All the money raised will be used to help young Japanese artists who want to study in the United States.
The cup was put on "Yahoo! Japan Auctions" at midday Monday, with the starting price of one yen. The auction is set to finish at 1400 GMT Sunday.
By Tuesday morning, more than 500 bids had been placed, with the top offer at more than 4.1 million yen. The auction can be followed at http://page3.auctions.yahoo.co.jp/jp/auction/c323847712
The quake-tsunami catastrophe killed some 19,000 people on Japan's northeast coast and sparked the world's worst nuclear accident since the 1986 Chernobyl disaster, leading to a plunge in visitors to the country.
The songstress visited Japan twice after the disaster and called on tourists from around the world to follow suit.
She is due back in Japan next week as part of an Asian tour.