"There is tension between us and the U.S. government on issues of civilian casualties, arrests of Afghans, nightly raids on homes and the casualties they cause," Karzai told al-Jazeera television in an interview Friday.
Obama has said the U.S. will increase its attention on Afghanistan under his tenure as the U.S. transitions out of Iraq. But the administration is still debating how to stem the Taliban tide and tackle the endemic corruption in Karzai's government more than seven years after the 2001 invasion.
Taliban militants have increased attacks and swept up wide areas of countryside over the last three years. The U.S. is contemplating sending up to 30,000 more American forces to back up the 33,000 already in Afghanistan.
Richard Holbrooke, Obama's new envoy to Afghanistan and Pakistan, has met with Afghan lawmakers and officials, international military leaders and U.N. diplomats during a fact-finding trip that began Thursday.
Holbrooke on Saturday met with Foreign Minister Rangin Dadfar Spanta and was to meet later with Karzai. Holbrooke has made no public comments during the Afghan leg of his trip. He previously visited Pakistan and also is to stop in India.
Karzai in recent weeks has publicly pressed the U.S. to use Afghan troops on nighttime raids in order to prevent civilian casualties. Karzai's public criticism of the raids and the civilian deaths caused by U.S. troops has added to recent tensions in the U.S.-Afghan relationship.
The U.S. military and Afghan Defense Ministry announced Thursday that Afghan officials and troops would take greater part in U.S. missions, particularly night raids.
"There will be better coordination to minimize risk of civilian casualties and ensure Afghans search Afghan homes and conduct arrest operations," a joint U.S.-Afghan statement said. It wasn't yet clear how soon Afghans would be placed on those missions.