“These infiltrations are causing harm to friends and allies and cause harm to US troops. It will be a topic of conversation,” Mr Bush said at a news conference in Kabul after talks with Afghan President Hamid Karzai.
Mr Bush began his first visit to South Asia with a surprise stopover in Afghanistan.
Some 21,000 US-led soldiers are hunting for Al Qaeda and Taliban militants in the south and east of Afghanistan.
“My message to President Musharraf is that it’s important that we bring these people to justice. He understands it and after all they tried to kill him four times,” Mr Bush said.
About Al Qaeda leader Osama bin Laden and Taliban chief Mullah Omar, the US president said: “It’s not a matter of if they are captured and brought to justice, it’s when they are brought to justice.” .
Earlier in the day, Mr Bush’s Air Force One flew to Bagram air base, headquarters of the US presence in Afghanistan, from where helicopters ferried him and his entourage across the dusty plain over mud brick homes to Kabul.
Mr Bush also visited the new premises of the US embassy in Kabul. During the ribbon cutting ceremony Mr Bush said: “It’s in our nation’s interest that Afghanistan develop into a democracy. It is in the interests of the United States of America for there to be examples around the world of what is possible.”
American officials have portrayed Afghanistan as a relative success story compared to the US front in Iraq.
Mr Bush said Washington was there for the long haul.
“My message to the people of Afghanistan is: take a look at this building — it’s a big, solid, permanent structure which should represent the commitment of the United States of America.”
Mr Bush said Afghans who visited Washington often asked him whether the US was committed to Afghanistan’s future.
“They ask me with their words, they ask with their stares as they look in my eyes, ‘Is the United States firmly committed to the future of Afghanistan’? My answer is ‘absolutely’,” he said.
TALIBAN CLAIM: The Taliban deputy leader Mullah Abdullah Akhund said that Bush’s ‘secret visit’ showed the Taliban had a strong control over Afghanistan. —AP/Reuters