The emergency declaration, which Obama signed late Friday, lets doctors and nurses temporarily bypass certain federal requirements so they can better handle a spike in influenza A(H1N1) patients.
The declaration comes just days after Health Secretary Kathleen Sebelius warned that demand was outstripping supply of vaccine for the novel flu strain.
"The 2009 H1N1 pandemic continues to evolve," Obama said in the declaration.
"The rates of illness continue to rise rapidly within many communities across the nation, and the potential exists for the pandemic to overburden health care resources in some localities."
US officials however said the declaration was not issued due to any specific development, but rather as a pre-emptive measure.
As Americans waited for more vaccine shipments, 46 of the 50 states now report widespread swine flu activity -- an unusually early uptick that ordinarily takes place in January or February at the peak of a normal flu season.
"By rapidly identifying the virus, implementing public health measures, providing guidance for health professionals and the general public, and developing an effective vaccine, we have taken proactive steps to reduce the impact of the pandemic and protect the health of our citizens," Obama said.
Among other things, the declaration gives Sebelius temporary authority to allow local authorities to set up makeshift emergency rooms to treat possible flu victims separate from regular patients.
In a note to Congress, Obama said the move was implemented "in order to be prepared in the event of a rapid increase in illness across the nation that may overburden health care resources."
At least 4,999 people have died from swine flu infections worldwide since April, when an outbreak was first reported in Mexico before rapidly spreading to the United States, according to the World Health Organization.
In the United States, Sebelius first declared a public health emergency in response to the virus on April 26, and renewed that declaration on July 24 and October 1.
"We are nowhere near where we thought we'd be by now," Centers for Disease Control and Prevention (CDC) chief Thomas Frieden said Friday of the amount of vaccine available.
Because of the vaccine shortage, the state of New York on Friday suspended a contentious requirement for health care workers to be inoculated against swine flu by the end of next month, or risk losing their jobs.
As of Friday, the CDC had 16.1 million doses of swine flu vaccine ready for shipping, and more than 11 million doses have been sent out to state health authorities.
Around half of those were nasal mist, which can only be administered to healthy people between the ages of two and 49, and excludes those individuals particularly at risk of infection -- pregnant women, people with chronic respiratory illness like asthma and very young children