"I am sorry for not being with you," John Paul said, speaking in a weak voice and slurring his words. "I carry you all in my heart and I bless you with affection."
The Vatican said the disorder was "mild" but that it decided to have Cardinal Angelo Sodano, the Vatican secretary of state, represent the pontiff at the weekly audience.
Papal spokesman Joaquin Navarro-Valls said in an official statement that the pope had taken ill Tuesday afternoon with intestinal problems and that on the advice of his doctors had decided to scrap the audience.
Sodano read the pope's speech and then led the crowd in applauding after John Paul spoke from Castel Gandolfo.
Pilgrims shouted "Viva il papa!" or "Long live the pope!"
The 83-year-old pope suffers from Parkinson's disease, and has debilitating knee and hip ailments that have made it difficult for him to walk. His aides wheel him around in a throne-like chair for public appearances and to celebrate public Masses.
He has appeared weaker in recent months, and during his recent trip to Slovakia was unable to recite all of his speeches, leaving it to aides to finish them off for him.
As recently as Sunday, however, John Paul had appeared to be in better form, speaking clearly to hundreds of pilgrims who had gathered at Castel Gandolfo.
During that appearance, the pope spoke of his plans to visit a Marian shrine at Pompeii, in southern Italy, on Oct. 7.
The pope was at Castel Gandolfo and was to have traveled into Rome for Wednesday's audience. About midway through August, the pope started traveling into the capital for his audiences rather than hold them in the courtyard of Castel Gandolfo, which is smaller and warmer than the air-conditioned Vatican hall.
After his Oct. 7 Pompeii visit, the pope has a busy week surrounding the celebrations marking his 25th anniversary as pope, which will culminate with an evening mass Oct. 16 in St. Peter's Square. That anniversary will make him the longest-serving pope in a century, since Leo XIII, who led the church from 1878 to 1903.
Three days later, he is to preside over the beatification of Mother Teresa, the nun who devoted her life to caring for the destitute of Calcutta.
In the mid-1990s, the pope occasionally suffered from the flu and other intestinal problems that forced him to cancel appearances. The problems appeared to have been largely resolved after he had his appendix removed in October 1996.