With the new year, the nation's 361 ports will usher in new security standards--all in an effort to reduce their vulnerability to terrorism. But observers say the enhanced security measures could result in increased port fees, which will likely trickle down to smaller companies.

Importing and exporting companies and municipal port authorities were required to submit detailed safety reports to the Department of Homeland Security by December 29. After reviewing these documents, the Coast Guard and other agencies will now suggest ways to improve security, which ports will have until July 1 to adopt.

Already, some businesses have faced security surcharges, and the costs are likely to rise. The government has earmarked only $400 million so far for the estimated $7 billion port security tab. "This is really a shared burden," says Coast Guard spokeswoman Jolie Shifflet.

Companies looking to get out in front of this issue should explore joining the Customs-Trade Partnership Against Terrorism, which certifies members as safe port users, meaning they can avoid lengthy inspections of cargo and facilities. Some 4,500 businesses are participating in the voluntary program, and large corporations like Target are pushing for vendors to sign on. "It's going to get to the point where if you're not certified, you're the exception," says Port of Charleston spokesman Byron Miller.