Bach's statement, delivered at a sports conference in Denmark, comes a few months before the IOC chooses between China and Kazakhstan to host the 2022 Winter Games. Both countries are frequently criticized for their record on human rights and press freedoms.
Bach reiterated his position that the IOC must remain "politically neutral" but also consider the political implications in naming host cities.
"Choosing a host city does not mean that the IOC necessarily agrees with the political and/or the legal system in the host country," he said in the speech Thursday.
The IOC was criticized by human rights groups for giving the 2008 Olympics to Beijing and 2014 Winter Games to Sochi, Russia. In July, the IOC will choose either Beijing or the Kazakh city of Almaty for the 2022 Winter Olympics.
Bach said a host-city choice also "does not mean that we agree with the death penalty or with discrimination, just to name a few."
Among countries with the death penalty are Japan, which will host the 2020 Olympics in Tokyo, and the United States, which has entered a bid from Boston for the 2024 Games.
"In every country where we organize the Olympic Games, we want to send the strong message of tolerance, respect and fair play," Bach said. "It means that we require compliance with all the values of the Olympic Charter for all participants at the Olympic Games."
Bach noted that the IOC asked for and received assurances from Russia that a law prohibiting promotion of gay "propaganda" would not apply at the Sochi Games.
"This assurance was fully respected," he said.
He said the IOC has added language on non-discrimination on grounds of sexual orientation to Principle 6 of the Olympic Charter and included a new clause on human rights protection in the host city contract.
"It is the responsibility of the IOC to ensure the application of the Olympic Charter at the Olympic Games," Bach said. "At the same time, we must acknowledge that we have neither the mandate nor the capability to change the laws or the political system of a sovereign country.
"The IOC is neither a world government, nor a superior world parliament."
Bach criticized past political boycotts "which did not serve any good purpose," referring to the U.S.-led boycott of the 1980 Moscow Olympics and the Soviet-led boycott of the 1984 Los Angeles Games.
"Boycotts are a fundamental contradiction to the spirit of sport, depriving it of the means to work for peace, mutual understanding and solidarity," he said.