Jackson was in the capital to accept MTV Japan's "Legend Award" during an earlier ceremony at Yoyogi Olympic Stadium. There, he choked up as he thanked fans for their loyalty.
His visit to Japan is the first leg of an Asian swing that will include stops in Singapore; Shanghai, China; and Hong Kong.
After weaving through dozens of screaming adult fans outside the downtown orphanage, Jackson was ushered into a gymnasium where more than 160 children between the ages of 3 and 18 and nuns in gray uniforms waited.
"I love you," Jackson told the cheering crowd. Then he whispered to his translator, apparently asking how to say the phrase in Japanese. Then he said: "Aishiteru!"
At his appearance at the MTV Japan Awards, Jackson said he was honored to be in Japan and happy to be around Japanese people he said he loved very much. He thanked them for their loyalty.
Jackson has been living in Bahrain since his acquittal on child molestation charges in Santa Maria, Calif.
The Asian tour is being organized by Broderick D. Morris, chief executive of Positive Productions Yokohama, an entertainment promotions company, Bain said.
"Michael Jackson is a legend ... He loves Japan and we love him," Morris said in a press release. "We look forward to welcoming him."
Jackson was quoted as saying, "I look forward to my visit to Japan because I have so many fond memories of my visits there. I thank MTV Japan for this honor and Mr. Morris for spearheading this visit.
"I look forward to seeing old friends and saying hello to my huge fan base in Japan who, like my other fans around the world, have for so many years consistently shown their love and support to me and my family."
Spokesperson Raymone K. Bain said that Jackson plans to return to recording and hopes to release a new album in 2007. Meanwhile, she said work continues on the song he has planned as a charity fundraiser for victims of Hurricane Katrina.
By Linda Deutsch