Ending talks at Bush's Texas ranch, they also said they would work to ease Russia's concerns about a US missile shield in Eastern Europe aimed at countering threats from rogue states.
Afghan President Hamid Karzai has protested the rising civilian death toll from U.S. and NATO operations trying to defeat a spring offensive by the Taliban.
Afghan officials say dozens of civilians have been killed in recent weeks. The growing death toll has triggered protests by Afghans demanding Karzai's resignation and the expulsion of American troops from Afghanistan.
''The Taliban likes to surround themselves with innocent civilians,'' Bush said. ''They don't mind using human shields because they devalue human life.'' Karzai has said Afghanistan could no longer accept civilian casualties, and a US military commander apologized for the killing of 19 civilians by US soldiers during an attack in March.
The NATO-led International Security Assistance Force has about 37,000 troops in Afghanistan, including about 15,000 from the United States, according to the Pentagon. Germany has called for a review of the way Western forces operate in Afghanistan.
''Every innocent civilian fatality, death, is one too many,'' de Hoop Scheffer said. ''But in a conflict, it is, from time to time, unavoidable.'' He said NATO forces still had the support of a majority of the Afghan people, and that he had discussed the issue in a telephone conversation with Karzai a few days ago.
NATO forces were in a ''different moral category'' from the Taliban and insurgents who behead people and commit suicide bombings, he said.
''We still have very much the hearts and minds of the Afghan people, because they do see they do see that their nation, their own nation, has no future under Taliban rule,'' de Hoop Scheffer said.
Bush hosted the NATO secretary-general at his ranch in Crawford, Texas, giving him a mountain bike tour of his property today morning.
The leaders agreed to work to allay Russian President Vladimir Putin's concerns about US plans to build a missile shield in eastern Europe.
Russia said this month it would no longer inform NATO states about movements of troops on its territory, freezing its commitments under the Conventional Forces in Europe treaty because of the dispute over the missile shield.
''I will continue to reach out to Russia,'' Bush said.
He noted that he sent Defense Secretary Robert Gates to Russia recently to make sure they understood the missile shield was not directed at them, but rather at other countries that could ''affect the peace of Europe.''