TOKYO — The Prince and Princess of Wales went to church and were cheered by thousands of Japanese Sunday during their stay in Tokyo.

But millions more missed a glimpse of Charles and Diana because regular programming of baseball games, quiz shows and family dramas on television was not interrupted to showcase the visiting royal couple.

In the morning, they went to the Anglican-Episcopal St. Alban's Church, near Tokyo Tower. A crowd of about 300 waited across the street behind a double strand of yellow and black twine for the royal couple.

A single Union Jack was raised above the crowd and another hung from the window of an office building. Traffic was light and police loosened the grip on security — when compared with the checkpoints and electronic surveillance gear for the economic summit of a week before.

On one corner, a portable watchtower was manned by a single policeman. Others stood in groups to seal alleyways and other approaches to the church.

A motorcade of three motorcycles and a police car shepherded a black limousine with the golden chrysanthemum crest of the Japanese Imperial family on the door.

Charles and Diana got out, accepted bouquets from two small boys and walked to the doorway of the small, single-story church.

Charles wore a conservative gray-striped suit with a green tie and Diana was dressed in a cream and navy blue dress with a wide-brimmed hat of the same colors.

They were greeted at the doorway by Bishop John Watanabe, who heads more than 300 Anglican congregations in Japan, Bishop of Tokyo John Yamada and The Reverend Llewellyn F. Wray, rector of Saint Alban's Church. Some 200 parishioners waited inside.

British Embassy officials said services were brisk and simple — singing, Bible reading and prayers. Charles read out loud from the Bible during the service.

There was no live television coverage and all channels carried the regular morning run of dramas and variety shows — the same as the day before, when the Prince and Princess arrived at Haneda airport from Osaka.

A CROWD AT the airport saw then live, but NHK — an official government TV network — wasn't about to break into a Tokyo Giants baseball game.

Many children were in the crowd gathered outside the church, one a small girl in African costume. But no live-coverage cameras were trained on Charles and Diana when they came back out, received more bows and curtsies, and listened as Michelle McMullen, 16, the daughter of an American businessman, strummed a guitar and led the children in ''Jesus Loves Me."

Heaped with flowers, Charles and Diana paused to chat with some children with their parents, then walked to the car. The princess stopped there and responded to repeated shouts of "Diana-san" by walking across the street, followed by her husband, and grasping the hands of young schoolgirls.

THEY TRAVELED on to the Mitsukoshi Department Store and the Honda Motor Co. A crowd estimated by police at about 92,000 stood along a loop-shaped route to the state guest house in Akasaka, looking like figures in an animated cyclorama as they waved paper Japanese and British flags and cheered wildly.

Standing in an open limousine, Charles and Diana looked tired, but returned the waves of the crowd.

While at the Akasaka Palace, the rest of Sunday was taken up meeting with youth groups and seeing demonstrations of flower arranging and doll-making. This was followed by a trip to Kuramae Stadium to occupy the box of Emperor Hirohito and observe a traditional Japanese sport.

There, Charles and Diana were seen as incidental characters in the Summer Grand Sumo Tournament.

On Monday, the two were to tour the Nissan Motor Plant in suburban Zama, have lunch with Prime Minister Yasuhiro Nakasone and view kabuki, traditional Japanese theater. They were scheduled to leave Tokyo Tuesday.