Previously, Puerto Rico’s department of health had only reported about 35 cases in which a fetus was lost or baby was born with Zika-related birth defects, raising concerns that the extent of damage to infants has been underplayed on the island.

On a call with reporters, Dr. Anne Schuchat, the acting director of the C.D.C., replied, “We do believe that Puerto Rico authorities are doing a very good job right now in evaluating babies whose mothers had Zika infection, and characterizing them and reporting in.”

On Monday, Puerto Rico declared that its Zika epidemic had ended, based on data showing the number of new cases had fallen. Regardless, C.D.C. officials said today that they still advised pregnant women to avoid traveling to Puerto Rico and to protect themselves against mosquito bites, if they do.

“We do agree that the disease went up and it’s come down, but that the risk is ongoing and that’s why they are continuing intensive surveillance and outreach,” Dr. Schuchat said.

Dr. Tom Frieden, the former director of the C.D.C., said of Zika, “It may not be epidemic anymore, but it’s endemic” in Puerto Rico.

“What we often see with this type of infection, it’s really bad in the first year and less bad in future years,” he added. “That’s why C.D.C. has retained its travel guidance.”

Dr. Frieden also cautioned that this report “is a minimum estimate of the number of infants who may be Zika-affected,” in Puerto Rico, because not all women whose infections were confirmed in the first trimester have given birth yet.