On another potentially controversial matter, the president also issued a "signing statement" with the bill, saying several of its provisions raised constitutional concerns and would be taken merely as suggestions. He has criticized President George W. Bush for often using such statements to claim the right to ignore portions of new laws, and on Monday he said his administration wouldn't follow those issued by Bush unless authorized by the new attorney general.
White House officials have accused Bush of using the statements to get around Congress in pursuing anti-terror tactics.
Obama signed the bill in private, unlike a number of recent signings that took place with fanfare, but he raised the issue of earmarks in public remarks playing down their scope and possible harm in the measure. They comprise about 1 percent of the spending package, which will keep the government running through September, he told reporters.
"Done right, earmarks have given legislators the opportunity to direct federal money to worthy projects that benefit people in their districts. And that's why I've opposed their outright elimination," he said.
Still, the president acknowledged the storm of criticism from watchdog groups, talk show hosts and many Republican lawmakers - including some who have obtained earmarks - who call them wasteful and politically motivated. They are special provisions earmarking money in spending bills for specific projects.
Obama, too, has criticized them as overused and subject to abuse.
Proposing new safeguards, he asked Congress to require that any earmark for a for-profit company be subject to competitive bids. He also said he would work with Congress to eliminate earmarks or other specific items in spending bills that he believes serve no legitimate purpose. But he did not specify how.
Critics were unmoved. Obama "naively asked earmark addicts to police themselves," said Sen. Jim DeMint, R-S.C. Lawmakers "trumpet their pork on their Web sites," he said, "and nobody believes we will have public hearings on pet projects."
Presidents can ask Congress to rescind various spending items. But the authority has little bite because lawmakers tend to ignore requests to undo their work.
Sen. John McCain, Obama's GOP opponent in last year's election, wants to require Congress to vote on a president's rescission requests. Obama is open to such a change, spokesman Robert Gibbs said, but has not proposed it.
"It doesn't do anybody any good to send up a rescissions package," Gibbs said, if it "becomes a piece of paper in somebody's file drawer."
Congress has wrestled for years with how to regulate earmarks, the targeted spending items for construction projects, weapons systems, research grants and thousands of other programs sought by Senate and House members. Voters tend to disdain earmarks in the abstract, but they often embrace the money and jobs that earmarks produce close to home. Many lawmakers base their re-election bids on the goodies they steer to constituents, and efforts to eliminate earmarks have repeatedly met strong resistance in both parties.
Nearly all earmarks serve some public purpose, even the so-called "bridge to nowhere" in Alaska. But abuses have included tying earmarks to kickbacks, including those that sent former Rep. Randy "Duke" Cunningham, R-Calif., to prison in 2006.
Congress tightened regulations after that, including requirements that requests for earmark be made public and subject to scrutiny. The number has decreased since then, but they still totaled 7,991, costing $5.5 billion, in the "omnibus" spending bill Obama signed Wednesday.
The president called the bill imperfect and recommended further earmark changes "to ensure that the budget process inspires trust and confidence instead of cynicism."
For a time, President Bill Clinton enjoyed line-item veto power, which allowed him to strike specific projects, including earmarks, from massive spending bills. But the Supreme Court ruled it unconstitutional in 1998. Since then, presidents have had to accept or veto entire spending bills, often packed with thousands of items, some of them earmarks.
Congress' Democratic leaders issued statements Wednesday praising Obama's remarks and defending earmarks in general. The House Appropriations Committee announced said it would submit every future earmark to the appropriate executive branch agency for a review.
But a statement issued by the committee's chairman, David Obey, D-Wis., hinted at irritation with the public's focus. "With all of the hyperventilating over the 1 percent of the omnibus appropriations bill that is made up of earmarks," he said, "Washington has mostly glossed over the important results it has achieved with the other 99 percent of the bill."
It was unclear how Congress might prevent earmarks from being directed to specific for-profit companies. House Appropriations staffers said the process will be changed to prevent "sole-sourcing" of contracts through earmarks and to require an open bidding process instead.
Obama's signing statement said he wouldn't be bound by provisions of the bill in five areas. They involved negotiations with foreign governments, limits on using U.S. troops in U.N. missions, protections for government whistleblowers, a congressional claim of authority over the spending of money already approved by Congress and congressional demands that the administration submit budget requests in certain forms.
Associated Press writers Andrew Taylor and Jennifer Loven contributed to this report.
The San Diego Police Department has launched an internal investigation into a program intended to reward officers for making drug arrests.
Police were involved a pursuit late Saturday that ended with a deadly officer-involved shooting in Escondido.
Two people died early Sunday morning after a high-speed chase ended in a head-on crash in North County.
A man was shot and killed by police at an officer- involved shooting in Escondido, a sheriff's lieutenant said Sunday.
An approaching winter storm is poised to open an "atmospheric river" of subtropical rain clouds on Southern California this week, but the San Diego area is expected to see just a fraction of that moisture, forecasters said Sunday.
A man threw rocks at vehicles on Interstate 5 near Imperial Beach Sunday, and threatened police with a pickaxe as he ran into a riverbed.
San Diego Sen. Toni Atkins will make history Wednesday when she becomes the first woman and first lesbian to hold the California Senate's top job.
A 16-year-old boy was allegedly drunk when he crashed his car into a stopped vehicle, pinning a motorist between two bumpers, police said Sunday.
A 27-year-old man suffered fatal injuries as the result of a "punching game'' inside of a bar Saturday morning in the Gaslamp
neighborhood of San Diego.
A large plume of smoke filled the sky in Miramar on Saturday morning after a concrete supply building went up in flames.