The Hoffman Estates, Ill., retailer said in a statement it reviewed a transcript of the show and found Mr. Maher and his guests described the U.S. military as "cowardly."
Lee Antonio, a spokeswoman for Sears, said the retailer pulled national advertising on the ABC program following a large number of complaints from Houston customers. The show is carried on Channel 13 in the Houston area.
"Bill and his guests have every right to say whatever they want to say," she said. "We have the freedom to advertise where we feel best to reach our customers."
In a statement, Mr. Maher said, "In no way was I intending to say, nor have I ever thought, that the men and women who defend our nation in uniform are anything but courageous and valiant.
Mr. Maher went on to say that his criticism was meant for "politicians who, fearing public reaction, have not allowed our military to do the job they are obviously ready, willing and able to do, and who now will, I'm certain, as they always have, get it done."