"It's a huge disappointment for us," said Agosto, who injured his back. "We had been looking forward to defending our title once again at the U.S. championships. However, the good news is that I am making progress, and I hope to begin training again in a few weeks."
The 2009 championships are scheduled for Jan. 18-25 in Cleveland.
Belbin and Agosto won the silver medal at the 2006 Winter Olympics.
"Ben is making steady progress," Belbin said. "While he recuperates, I am continuing to train hard on my own, so I am certain that we'll be in top shape before March. We have requested that U.S. Figure Skating consider us for the U.S. World Team."
Belbin and Agosto are planning to compete in the 2009 World Figure Skating Championships in Los Angeles March 22-29.