Taylor's administration has been accused of executing political opponents, conscripting boys into child armies, and forcing girls into prostitution.
Woewiyu's Philadelphia-based immigration lawyer, Raymond Basso, said Tuesday that his client took no part in the more brutal aspects of Taylor's campaign to control the African nation, founded by freed U.S. slaves in 1822.
"Tom had nothing to do with any of that," Basso said. "Immigration and the U.S. government were fully aware of that."
Woewiyu has maintained legal residency in the United States since 1972, while shuttling back and forth between here and Liberia - at times even serving as its labor minister and president pro tempore of its Senate.
Woewiyu was returning from a trip to Africa, where he is pursuing another Senate term, when U.S. Homeland Security agents detained him Monday at Newark Liberty International Airport.
Woewiyu and his family appeared confused by his arrest at an initial appearance in federal court in Philadelphia on Tuesday. Basso rushed into the courtroom midway through the proceedings, saying he had only learned of the hearing 10 minutes earlier.
"I've been getting all these calls from the Liberian press," said Thompson Dahnsaw, Woewiyu's son-in-law. "Nobody knows what is going on."
In announcing the arrest, prosecutors took a hard tone, labeling Woewiyu a war criminal.
Though he is only charged with lying to immigration authorities, the case is being investigated by a U.S. Immigration and Customs Enforcement unit focused on human-rights violators and those who have sought to hide in the country after taking part in genocide or torture.
Woewiyu has lived comfortably as a legal permanent resident in Delaware County for much of the last four decades, Basso said Tuesday.
He first arrived in the area in the '70s, when he - along with many young Liberians, including Taylor himself - arrived to attend college in the United States.
Woewiyu earned a bachelor's degree in labor studies from Rutgers University in 1981 and is pursuing a master's degree from Pennsylvania State University. He has made his living through real estate investment.
He first applied for citizenship in 2006, submitting a form that prosecutors now say contained many misrepresentations.
Asked whether he had ever advocated the overthrow of another government, Woewiyu said no. He also allegedly failed to mention his association with Taylor when asked whether he had ever engaged in political persecution, according to the indictment.
But Basso on Tuesday questioned why prosecutors had waited eight years to bring a criminal case against his client.
Homeland Security agents interviewed Woewiyu in 2010 for nearly four hours about an unrelated case, the lawyer said. He described that meeting as "cordial."
And though Woewiyu's citizenship application had been denied in 2009, federal authorities did not indict him until January or arrest him until Monday.
"I don't know," Basso said. "Politically, it's not very popular to be tied to Charles Taylor right now."
Inquirer staff writers Jeff Gammage and Mari A. Schaefer contributed to this article.