The declaration allows the US Department of Health and Human Services to award grants, access emergency funds and temporarily appoint personnel where needed, among other things.
"This administration is committed to meeting the Zika outbreak in Puerto Rico with the necessary urgency," Secretary Sylvia Burwell said in a department statement. Burwell traveled to the US territory in late April to evaluate its response to the outbreak.
A department spokesman did not immediately return a message seeking comment on what immediate steps the agency may take.
The mosquito-borne virus has infected 1,035 pregnant women, which is a concern to authorities because Zika has been tied to a severe birth defect known as microcephaly. More than 100 pregnant women infected with Zika in Puerto Rico who have given birth have had healthy babies, officials said.
Puerto Rico reported the first microcephaly case acquired on US soil in May, involving a dead fetus that a woman turned over to health authorities. Since then no microcephaly cases have been reported, but federal officials say it's only a matter of time.
"Zika poses a hidden threat to future generations of Puerto Ricans, and I feel the responsibility to do everything in my power to fight the spread of it," he said.
Garcia recently authorized the use of Bti, an organic larvicide, to fight the spread of Zika after rejecting aerial spraying with the insecticide naled as proposed by the US Centers for Disease Control and Prevention.
Puerto Rico Health Secretary Ana Rius said 90 people have been hospitalized because of Zika. Officials also say 30 people have been diagnosed with a temporary paralysis condition known as Guillain-Barre that has been linked to Zika.
The emergency was declared one day after the US surgeon general visited Puerto Rico and said he expected 25 per cent of Puerto Rico's nearly 3.5 million people will be infected with Zika by year's end.
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