I'm honestly not sure. It's clear here that he's talking about his role in the aftermath of the anthrax attacks, not the September 11 attacks. The Thompson campaign is saying this, according to the National Journal:

Thompson spokesman Brian Nemoir said in a statement that, "as a point of clarification, 9/18/01 is in reference to the anthrax attacks on specific members of congress and varied members of the news media. In-total, it is believed that seven letters were mailed containing anthrax spores, contaminating 22 people of which five people died. As Secretary of the Department of Health and Human Services, Tommy Thompson lead the efforts to protect our nation from these bio-threats."

Which is plausible, if Brian hadn't told the HuffPo this first:

"There are two plausible explanations as to the recent 9/18 versus 9/11 reference made by Tommy Thompson at a recent event," said campaign spokesman Brian Nemoir. "First, the entire civilized world has the wrong date of this historic and tragic attack on our nation's soil; second, during a spirited campaign appearance Tommy Thompson misspoke regarding an horrific episode in our country’s history during which he played a key leadership role. The campaign is fully examining both scenarios."

I know Brian, and Brian I'm sorry, but that first answer was 50 shades of idiotic. If it was meant as a joke it was idiotic. If it was meant as a serious answer, it was idiotic. The anthrax attacks did, in fact, begin on Tuesday, September 18th, one week after the 9/11 attacks. It's entirely possible that's what Tommy was referring to and Brian spoke with HuffPo before actually asking Tommy what happened. If Brian did that, it was a hopelessly stupid thing to do.