President Bush has telephoned his Pakistani counterpart to discuss tensions between Pakistan and Afghanistan over the war on terror.
This was Mr Bush's first intervention in the current dispute
Afghanistan urged Pakistan on Tuesday to crack down on Taleban fighters it says are sheltering on its soil.
The Afghan presidential spokesman said "terrorists" were being trained in Pakistan. His remarks follow a recent upsurge in violence in Afghanistan.
Afghanistan also says it has foiled a plot to kill the US envoy in Kabul.
That was followed by renewed criticism from Kabul of Pakistan's anti-militant efforts.
Islamabad said allegations it was not doing enough to fight the militants were "irresponsible and baseless".
President Bush spent 15 minutes on the phone to President Pervez Musharraf, Pakistan's information minister Sheikh Rashid Ahmed said.
After that, President Musharraf called Afghan President Hamid Karzai to "remove the misunderstanding" resulting from recent events, including the arrest of several suspected Pakistani militants in Kabul, Sheikh Rashid said.
The information minister said that Pakistani could not be held responsible for the acts of individuals involved in "illegal activities".
Correspondents say this is a reference to the three Pakistanis arrested over an alleged plot to kill the US ambassador to Kabul, Zalmay Khalilzad.
In violence on Tuesday, Afghan security forces killed at least 11 suspected Taleban fighters in Kandahar province, officials said.
Elsewhere in the province, an Afghan election officer was killed and another wounded when their vehicle was ambushed.
Afghanistan has seen a string of attacks and clashes in recent months in which scores of people, including at least 29 US troops, have died.
Most of the bloodshed has been in the south and east, bordering Pakistan.
"Our people are dying, our schools are getting burned, our mosques are getting blown up and our clergy are getting assassinated," Afghan presidential spokesman Jawed Ludin told a news conference in Kabul.
"Some provinces of the country, especially in regions that are close to Pakistani soil, are insecure in many ways.
"We need Pakistan and Pakistan needs us and then we both... need the rest of the world to join hands together to fight terrorism."
Three Pakistanis accused of trying to kill the US envoy to Kabul
Earlier on Tuesday Pakistan's government denied it was involved in unlawful activity on Afghan soil, or that there were Taleban leaders hiding in Pakistan.
Sheikh Rashid Ahmed told the BBC that if Pakistanis had been caught by the Afghans they should be tried.
He said Pakistan had always supported the government of President Hamid Karzai, despite having "to pay a huge price for it".
Thousands of Pakistani troops have been deployed in lawless tribal regions along the border in the hunt for militants.