To fix the Bureau of Customs, President Benigno S. Aquino III needed a numbers guy, someone who could make sense of the thousands of shipments and billions of pesos passing daily through the Philippines' ports.

He turned to John P. Sevilla.

Three months after taking over as commissioner in December, Mr. Sevilla told The Wall Street Journal he had been "shocked" by the Bureau's failure to analyze the rich data it received, information that held vital clues to its endemic corruption problems.

"I'm amazed that nobody bothered to put the data together until about a month ago," Mr. Sevilla said. "But we found out that we open up less than 1% of [shipping] containers, but of the containers that we open, 90% have problems."

He was also incredulous that Customs lacked a single reference source to help examiners make complex calculations about duties and fees incurred by traders. One is now being compiled, Mr. Sevilla said, "to make it easier for people to do their jobs…so that they have no excuse" for undercharging importers, a common practice rewarded with illegal payments.