The protester seated near the back of the auditorium stood up during Wen's speech and shouted: "How can you listen to this unchallenged?" before throwing a shoe that landed some distance from the premier.
Wen looked unruffled, paused a few seconds and then continued with his remarks. One of his aides quietly stepped on the stage, picked up the gray athletic shoe and removed it.
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University officials quickly escorted the protester from the auditorium. Police arrested the man on suspicion of a public order offense.
"The university is a place for discussion, debate and considered argument, not for shoe throwing," said Tim Holt, a university spokesman.
The protester was taken to a local police station for questioning, police spokeswoman Shelly Spratt said.
In a similar incident, an Iraqi reporter threw his shoes at former President George W. Bush during a news conference in Baghdad in December.
Iraqi journalist Muntadhar al-Zeidi was scheduled to face trial in December on a charge of assaulting a foreign leader, but the court date was postponed after his attorney filed a motion to reduce the charges. He remains in custody in Baghdad.
Here's a video of the incident: