The ports of Long Beach and Los Angeles will begin collecting “clean trucks” fees on Feb. 18, despite numerous delays imposed by federal regulators and pending court cases that could derail plans to clean up pollution at the ports.

“It’s imperative that we start the program and continue the progress we have made to date in terms of banning pre-1989 trucks and accelerating the deployment of more than 2,200 2007-compliant trucks through our 2007-Compliant Incentive Program,” said Port of Los Angeles Executive Director Geraldine Knatz in a Thursday statement. Long Beach port officials made their announcement on Wednesday.

The Clean Trucks Fee, which will charge the cargo owner $35 per standard 20 foot cargo container, is a central part of the Clean Trucks Program. That program aims to reduce diesel truck emissions by 80 percent by requiring all big rigs to comply with 2007 federal emissions standards within five years. The program started officially on October 1.

Collection of the Clean Truck Fee was scheduled to begin in November, but was delayed twice due to reviews of the program ordered by Federal Maritime Commission, the government agency that oversees the nation’s ports. After requesting more information about the plan from the ports, the commission ordered an initial 45-day review, and then a second 45-day review, which concludes Feb. 13. The port decided to start charging the fee after the expiration of the second review.

Meanwhile, the FMC has filed a lawsuit to block portions of the Clean Trucks Program as “anti-competitive” to business. U.S. District Court Judge Richard J. Leon said he would not rule on the FMC’s request for a preliminary injunction until sometime in 2009, and lawyers for both sides await a decision any day now. A port spokesman said collection of the fees could be stopped if the court so orders.

Some trucking companies have said that the delays are hurting them because they have bought expensive new clean trucks but haven’t been able to charge the clean truck fee to the cargo owners, which would help them meet their truck payments.

Port officials are frustrated too, saying once they collect the fee, they can reimburse more trucking companies that buy clean trucks in the future.

The Clean Trucks Fee is expected to raise about $1 million a day and help finance the replacement of many of the 17,000 trucks that service the port, officials said.