Obama signed the declaration late Friday, which the White House said allows medical treatment facilities to better handle a surge in flu patients by waiving federal requirements on a case-by-case basis.
"The foundation of our national approach to the H1N1 flu has been preparedness at all levels -- personal, business, and government -- and this proclamation helps that effort by advancing our overall response capability," the White House said in a statement.
In the proclamation, Obama said the pandemic keeps evolving, the rates of illness are rising rapidly in many areas and there's a potential "to overburden health care resources."
Because of vaccine production delays, the government has backed off initial, optimistic estimates that as many as 120 million doses would be available by mid-October. As of Wednesday, only 11 million doses had been shipped to health departments, doctor's offices and other providers, according to the federal Centers for Disease Control and Prevention.
The government now hopes to have about 50 million doses of vaccine for the so-called swine flu out by mid-November and 150 million in December.
"We are nowhere near where we thought we'd be by now," CDC Director Thomas Frieden said Friday. "We share the frustration of people who have waited in line or called a number or checked a Web site and haven't been able to find a place to get vaccinated."
The flu virus has to be grown in chicken eggs, and the yield hasn't been as high as was initially hoped, officials explained.
H1N1 is more widespread now than it's ever been. Health authorities say almost 100 children have died from the flu, and 46 states now have widespread flu activity.
Worldwide, more than 5,000 people have reportedly died from swine flu since it emerged this year and developed into a global epidemic, the World Health Organization said Friday. Since most countries have stopped counting individual swine flu cases, the figure is considered an underestimate.
The flu has infected millions of Americans and killed nearly 100 children in the U.S. The chief of the Centers for Disease Control and Prevention said Friday that over a thousand people have died as a result, with 46 states reporting widespread H1N1 activity.
"Since the beginning of the pandemic, we've seen more than 1,000 deaths and 20,000 hospitalizations," Frieden said. "We expect it to occur in waves, but we can't predict when those waves will happen."
The Associated Press contributed to this report.