The ports of Los Angeles and Long Beach began turning away truckers last week who have not registered under guidelines set in their controversial and repeatedly delayed truck replacement programs.

Roughly one in five trucks about 1,000 in all were denied entry to the ports Wednesday, resulting in major traffic tie-ups around the harbor.

“We know there would be problems, but everyone had enough time to know it was coming,” said John Holmes, director of operations for the Port of Los Angeles. “There is no grace period this time.”

Also on Wednesday, the ports began collecting the $35 cargo fee for all loaded trucks entering or leaving any marine terminal. The expense is being paid by cargo owners for all containers except those hauled by privately funded “clean” trucks compliant with 2007 federal emissions standards.

The Clean Truck Fee will go toward funding the purchase of new low-emissions trucks to help meet goals set in the Clean Trucks Program, which aims to cut diesel pollution by 80 percent in five years. The ports expect to see $9 million generated per month from the fee collection, a figure recently lowered after cargo shipments slumped by more than 10 percent last month.

The fee collection, monitored by an electronic gate access system using radio frequency identification technology, generated an initial outcry among cargo owners who said the fees would drive up the price of shipping goods.

Port officials maintained that the collection process has been smooth in the early going. Long Beach spokesman Art Wong noted that while 1,000 trucks were turned away, about 80 percent roughly 4,000 made it through the gates on the first day with no problems. By the second day, 90 percent of the trucks entered terminals without a problem.

Drivers were turned away primarily because they didn’t register their trucks in time or the cargo owners failed to pay the fee.

Drivers denied access were sent to the ports’ Truck Tag Replacement Center near Terminal Island, where on Wednesday the truck backup shutdown all the westbound lanes of the Gerald Desmond Bridge for a few hours, prompting the Port of Long Beach to issue a public statement urging people to avoid the area.

Traffic is expected to remain heavier than usual on Terminal Island, but officials said they’re anticipating almost all trucks will be able to enter by the end of this week.

Fee collection has been delayed three times: first by port authorities because of technical glitches, and twice by the Federal Maritime Commission, which oversees the nation’s ports, because it wanted to study the fee’s economic impact but two weeks ago signaled the ports could proceed.

In the run-up to Wednesday, port authorities bombarded drivers, trucking companies and cargo owners with pamphlets, phone calls and personal visits asking them to register, Holmes said.