William A. Ackman, the activist investor, has described his billion-dollar bet and continuing crusade against the nutritional supplements company Herbalife as a “moral obligation.” In at least one presentation, he nearly cried onstage and said that if his Herbalife trade was successful, he would give the profits to charity because he would consider them “blood money.”

Over the years, Mr. Ackman has made the case that his investments are guided by a strict moral code. He says he believes that Herbalife is a pyramid scheme targeting low-income people, and has resolved to bring it down because people hurt by the company “are not in a position to defend themselves.” He has also said he won’t invest in Coca-Cola because, “I think it’s bad for children and bad for people.”

And yet Mr. Ackman has spent the last several weeks defending his investment in Valeant, a pharmaceutical company whose financial practices have come under scrutiny and that is under federal investigation for its drug pricing and distribution practices. In two cases, Valeant acquired two old heart drugs and increased their prices, one by more than 500 percent and the other by more than 200 percent.

“The biggest regret I have with Valeant is that we’re not in a position to buy more,” Mr. Ackman told his investors in a call on Monday. In a letter to Valeant’s chief executive, J. Michael Pearson, he said, “You are one of the most shareholder-oriented C.E.O.s I know. You have assured me that you and the rest of the board are considering any and all alternatives that would benefit shareholders and other stakeholders. That is very comforting to us.”