Bai Yun's first cub was born on Tuesday at 1.15pm (local time). Zoo officials said it was common for twin panda births to occur up to 12 hours apart.
But more than 24 hours later, the signs that Bai Yun was in active labour began to diminish, zoo veterinarian Don Lundberg said.
"This is not the normal course of events for the species," Lundberg said. "We are simply letting nature take its course."
Tests performed 10 days ago indicated that both cubs were alive, zoo officials said.
"We assume the fetus is still in her body," Lundberg said. "We assume that she will eventually pass it. What we cannot tell you is if it will be alive or stillborn."
Although it is not uncommon for pandas to give birth to twins, female pandas sometimes reject the latecomer because they are unable to care for more than one cub at a time, zoo officials said.
"We assume the foetus is still in her body. We assume that she will eventually pass it. What we cannot tell you is if it will be alive or stillborn"
Zoologists were thrilled when a sonogram revealed on 4 August that Bai Yun, a 13-year-old female panda on loan from China, was pregnant with twins, although they were unsure which of two male pandas was the father.
In March, Bai Yun mated naturally with her new partner, Gao Gao. She also was artificially inseminated with semen from her former mate, Shi Shi, when Gao Gao lost interest after just one day.
In 1999, Shi Shi and Bai Yun became the parents of 3-year-old Hua Mei, the only surviving giant panda born in the United States.