Gil Kerlikowske, the director of the Office of National Drug Control Policy, called the 9 percent increase in drug use disappointing but said he was not surprised given "eroding attitudes" about the perception of harm from illegal drugs and the growing number of states approving medicinal marijuana.
"I think all of the attention and the focus of calling marijuana medicine has sent the absolute wrong message to our young people," Kerlikowske said in an interview.
The annual report from the Substance Abuse and Mental Health Services Administration found marijuana use rose by 8 percent and remained the most commonly used drug.
Mike Meno, a spokesman for the pro-legalization Marijuana Policy Project, said the survey is more proof that the government's war on marijuana has failed in spite of decades of enforcement efforts and arrests.
"It's time we stop this charade and implement sensible laws that would tax and regulate marijuana the same way we do more harmful - but legal - drugs like alcohol and tobacco," Meno said.
On a positive note, cocaine abuse continues to decline, with use of the drug down 32 percent from its peak in 2006.
About 21.8 million Americans, or 8.7 percent of the population age 12 and older, reported using illegal drugs in 2009. That's the highest level since the survey began in 2002. The previous high was just over 20 million in 2006.
The survey, which was being released Thursday, is based on interviews with about 67,500 people. It is considered the most comprehensive annual snapshot of drug use in the United States.
Other results show a 37 percent increase in ecstasy use and a 60 percent jump in the number of methamphetamine users. In the early 2000s, there was a widespread public safety campaign to warn young people about the dangers of ecstasy as a party drug, but that effort declined as use dropped off.
"The last few years, I think we've taken our eye off the ball on ecstasy," Kerlikowske said.
Meth use had been dropping after a passage of a 2006 federal law that put cold tablets containing pseudoephedrine behind pharmacy counters. But law enforcement officials have seen a rise in "smurfing," or traveling from store to store to purchase the medicines, which can be used to produce homemade meth in kitchen labs.
Kerlikowske attributed the rise in meth abuse to more people getting around the law and an increase in meth coming across the border with Mexico.
The rise in marijuana use comes as California voters prepare to decide in November whether to legalize the drug. An Associated Press-CNBC poll earlier this year found that most Americans still oppose legalizing marijuana, but larger majorities believe it has medical benefits and want the government to allow its use for that purpose.
Medical marijuana sales in the 14 states that allow it have also taken off since the federal government signaled last year that it wouldn't prosecute marijuana sellers who follow state rules. The survey does not distinguish between medicinal and non-medicinal marijuana use.
The survey found the number of youths aged 12-17 who perceived a great risk of harm from smoking marijuana once or twice a week dropped from 54.7 percent in 2007 to 49.3 percent in 2009.