US officials say the new Pakistani government's pursuit of peace deals with tribes along the porous Pakistani-Afghan border has allowed fighters to regroup and stage attacks on US forces in Afghanistan.
Earlier on Monday, Dana Perino, the White House spokeswoman, said that Bush believed that Pakistan recognised the fighters "are a threat to the Pakistanis themselves - not just to the United States or others".
"Does the president think they are doing enough? I think the president thinks we all need to be doing more," she said.
Bush also said ahead of his meeting with Gilani that he was "troubled" by the movement of fighters from Pakistan to Afghanistan and would discuss the threat with Gilani, who is making his first Washington visit since Pakistan formed a new coalition government in March.
Pakistani officials say they are working to forge agreements that would require tribes to surrender their weapons, withdraw support for foreign fighters and end attacks across the border from the tribal region, where Osama bin Laden, the al-Qaeda leader, is thought to be hiding.
But the government has also resisted proposals to allow US or other foreign troops in to the border region.
There has been growing speculation that the US is prepared to launch military "hot pursuit" raids into the region against fighters.
Monday's missile attack on a religious school in Azam Warsak village in the district of South Waziristan left six dead, including three foreigners, Pakistani intelligence officials told Reuters news agency.
There was no immediate claim of responsibility, however the incident follows a series of strikes apparently by US aircraft in recent months against fighters in the region.
US state department and White House officials told Al Jazeera they had no information on the incident, however both US forces based in Bagram base in Afghanistan and members of the International Security Assistance Force (Isaf), the Nato-led security mission in Afghanistan, denied involvement.
Last month a US air raid killed 11 Pakistani border troops, which led to angry protests from the Pakistani government.