Karzai's own brother, Ahmed Wali Karzai, has been at the center of allegations that he was involved in drug trafficking.
In a report citing unidentified sources, The New York Times said that the younger Karzai was a suspected opium trafficker and had received payments from the CIA.
Ahmed Wali Karzai told the Associated Press in a recent interview that the allegations were untrue and that his accusers were political and tribal enemies.
Secretary of State Hillary Rodham Clinton said on her trip to Kabul for Karzai's inauguration last week that she was concerned about some of the people he has surrounded himself with.
During his campaign, Karzai allied himself with Abdul Rashid Dostum, a warlord.
Obama told CNN in July that he had ordered an investigation into whether the Bush administration properly investigated allegations that Dostum killed hundreds of Taliban prisoners in 2001.
At his inauguration last week, Karzai said he would require senior government officials to register their assets and would dismiss any government officials involved in drug trafficking.
The U.S. ambassador to Afghanistan, Karl Eikenberry, has said the government needed to follow up rhetoric with results. "Words are cheap," he said. "Deeds are required."
Doctor who refuses bribes
Public frustration with government extortion is increasing.
Tolo Television, a commercial station in Afghanistan, has started to encourage people to videotape public officials, such as police, taking bribes.
They have already received a couple of videos of police accepting bribes.
People are still afraid to report bribery, said Humanyoon Daneshyar, an anchor on a news magazine show. They fear being identified and are not confident the government could protect them.
Even when someone is caught, prosecution is difficult.
Ahmadi said his office had identified three traffic office workers who continued to take bribes despite the changes. The workers are well-connected, making firings difficult.
"We will have to do it in a tactful way," Ahmadi said.
Ahmadi said he would like to tackle construction permits next. It takes about six months and some 200 signatures to get a permit now, he said.
Meanwhile, some citizens are taking matters into their own hands.
Rahimullah Safi, a physician at Kabul's Wazir Akbar Khan Hospital, said patients and their families are harassed every time they walk through the hospital's front door by police and staff seeking bribes to get them admission or treatment.
"Corrupt people have surrounded the government," Safi said. "They are in charge. This is reality."
Safi, a thin, 40-year-old dressed in a threadbare sport coat, said he refuses to take payoffs even though many of his colleagues do.
"I studied medicine not to get rich, not to take bribes," he said. "I studied medicine to help people."