Security officials told the BBC they are on 'high alert' for the meeting
Pakistani President Pervez Musharraf says he will not attend a three-day "peace jirga", or tribal council, in the Afghan capital Kabul.
Elders from the Pakistani tribal regions of North and South of Waziristan have also refused to attend.
Up to 700 tribal elders, Islamic clerics and leaders of both countries are invited to the council, starting on Thursday, which will discuss terrorism.
The Taleban have not been included, and are calling for a boycott of the event.
Pakistan's foreign ministry issued a statement on Wednesday saying Gen Musharraf had telephoned Afghan President Hamid Karzai to assure his "full support in making the Joint Peace Jirga a success".
But he said engagements in Islamabad meant that he would not be able to attend the council.
Correspondents say the decision may be intended as a snub to the US-sponsored jirga, following recent statements by US presidential candidates about alleged Pakistani failings in the "war on terror".
The jirga is also widely seen as a non-starter by the Pakistani establishment without the inclusion of the Taleban, they say.
A spokesman for Mr Karzai said building peace and stability was still the council's intention.
Gen Musharraf is sending Prime Minister Shaukat Aziz in his place to inaugurate the assembly along with Mr Karzai.
US State Department spokesman Sean McCormack did not rule out the Pakistani president's attendance later on.
"We'll see if President Musharraf is able to attend any portion of the meeting," he said.
The idea of a joint Afghan-Pakistan Peace Jirga was first suggested by Mr Karzai during talks with US President George W Bush in September.
In October, President Karzai said he saw the jirga as an attempt to revive Pashtun civil society on both sides of the border, to combat what he called the growing Talebanisation of the region.
Jirgas are a traditional method of decision-making and dispute-resolution. The Taleban have denounced the jirga, calling it "George Bush's initiative".
Supporters of the Taleban say talks that do not include them could be futile.
Abdul Ghafoor Haideri, secretary general of Pakistan's Jamiat Ulema-e-Islam (JUI) told the Associated Press news agency: "This is only a display, which cannot produce the true views of the Afghan people."
Tribal elders in north and south Waziristan on the border with Afghanistan have also said they are boycotting the jirga.
The BBC's Bilal Sarwary, however, said there was some optimism in Kabul.
The Afghan spokesman for the jirga, Asif Nang, explained that the jirga would look at "what causes the insecurity, locate the hideouts of terrorists, track finances and find out how we could deal with the whole problem".
Our correspondent says the sight of Pakistani flags throughout the city is unusual because of the climate of mistrust between the two countries.