updated 7/10/2008 1:24:16 PM ET 2008-07-10T17:24:16

A cargo ship's chief engineer and the companies that own and operate the vessel were charged Wednesday in federal court with using "magic pipes" to illegally dump oil and other harmful waste into the ocean.

Pantelis Thomas is charged with four counts of falsifying log books and other charges related to illegal dumping. His attorney Douglas Schwartz said Thomas plans to plead not guilty when he appears in U.S. District Court in San Francisco on Thursday.

Casilda Shipping of Malta owns the vessel and the Greek company Genesis Seatrading Corp. operates it. Both companies were charged with the same crimes along with three other charges accusing them of illegally dumping waste.

Brian McCarthy, a Port Washington N.Y. attorney identified in court records as representing the shipping companies, couldn't be reached late Wednesday for comment.

According to the indictment and court documents filed by the Coast Guard and Justice Department, the 626-foot Rio Gold arrived at the Port of Oakland on May 26 after dropping off a load of cement in Hawaii.

U.S. Coast Guard Lt. Daniel Every said in a court document that crew members complained to him that Thomas ordered them to discharge oily waste from the engine room directly into the ocean. Typically ships process the waste on board before disposing it onshore or burning it on board.

Crew members told the Coast Guard lieutenant that Thomas ordered them to construct "magic pipes" that bypassed standard procedures and dumped the waste directly into the ocean.

One of the crew members turned over a photograph of one such pipe taken with his mobile telephone while the ship was steaming toward Oakland.

Thomas, a Greek citizen, can't leave the U.S. until the case is resolved. His lawyer also said that at least eight foreign crew members who will serve as witnesses are also being prohibited from leaving the country.

Copyright 2008 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

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