Karzai recently made a renewed push to jump-start peace talks with the Taliban, which ruled Afghanistan until late 2001 and since then has led a bloody insurgency against the U.S.-backed government in Kabul.
Karzai's visit to Islamabad - his first trip to the next door neighbor since last year's controversial presidential elections - has been preceded by a widespread recognition of the inevitable need to induct the Taliban in a future ruling structure, reports CBS News' Farhan Bokhari.
However, western diplomats warned, the U.S.-led alliance in Afghanistan has yet to finalize the terms of a reconciliation that will bring rival Afghan factions around the same table, Bokhari reports.
"Our allies are not talking the same language from time to time," Karzai told reporters. "This is really one of the problems. All along in the past eight years, part of Afghanistan's trouble is this lack of coordination in allies, not only on this question but on a lot of other questions, on the conduct of the war on terror, delivery of assistance to Afghanistan, on the coordination of assistance between the international quarters, on the question of reconciliation, reintegration."
Pakistan has offered to help negotiate with the militants. But many observers believe Afghanistan wants to keep Pakistan out of any talks, suspicious of Islamabad's support of the Taliban government while the militants were in power.
Karzai tried to dispel that speculation during a joint news conference with Pakistani Prime Minister Yousuf Raza Gilani as part of a two-day trip to Pakistan - his first since he was re-elected in a fraud-marred vote last year.
He thanked Gilani "for offering support to Afghanistan's efforts for reconciliation," and added: "Indeed, Pakistan has a significantly important role to play there, and Afghanistan welcomes that role."
"Pakistan is a brother of Afghanistan," he said. "Pakistan is a twin brother of Afghanistan. We are more than twins - we are conjoined twins."
But such diplomatic hyperbole may mask Kabul's distrust.
Speculation over Pakistan's role in peace talks with the Taliban has increased in recent weeks following Islamabad's February arrest of the group's No. 2 leader in a joint raid with the CIA.
The, considered a likely channel in any talks with the top Taliban leadership, came as a surprise. He was one of the first senior Taliban commanders captured by Pakistan - even though many of the group's leaders are believed to be based in the country.
Critics have accused the Pakistani government of protecting Taliban leaders to maintain good relations with the group in anticipation of Western forces eventually withdrawing from the country - an allegation denied by Pakistan.
Some analysts have speculated the country was trying to guarantee itself a seat at the negotiating table.
"The Afghans see this as an undermining of their (peace) initiative," said Ahmed Rashid, a Pakistani expert on the Taliban.
At a Thursday breakfast meeting with reporters, Karzai called on Islamabad to hand over the Taliban commander, something Gilani said his government was considering.
Despite long-standing tension between the two countries, Kabul knows that Islamabad remains a powerful regional player and its longtime links to the Taliban could make it an indispensable part of talks.
"The Afghans are not in a position to take on Pakistan," said Rashid.
Karzai plans to hold a peace conference in Afghanistan in April that he hopes the Taliban will attend. He said Thursday he was dedicated to pursuing the process despite lukewarm enthusiasm from the U.S., which remains suspicious of talks with top Taliban leaders and prefers reaching out to disaffected Taliban fighters.
"Our allies are not talking the same language from time to time," Karzai acknowledged Thursday.
He said his government has had contacts within the Taliban leadership "as high as you wish to go." He would not say if that included Taliban leader Mullah Omar, but reiterated his willingness to talk to him.
Western diplomats based in Islamabad told Bokhari that Karzai's remarks highlighted a growing eagerness within the Afghan ruling structure to give a stronger nudge to a reconciliation process; however, there was still no evidence of the United States becoming equally enthusiastic.
One of the difficulties is what role the future has for Omar, Bokhari reports. The Taliban leader is known to be uncompromising on the question of withdrawing the group's support from al Qaeda.
"This is one of the major irritants between the Americans and the Taliban," said one European ambassador in Islamabad who spoke to Bokhari on condition of anonymity. "Mullah Omar must agree to abandoning al Qaeda before the Americans will even consider talking to him. Everyone, including the U.S. wants an end to the war in Afghanistan. But when we get down to the fine detail, the nitty gritty, that is where people recognize there are irritants which are not all that easy to solve."
Pakistan has long tried to influence Kabul to strengthen its regional position against its longtime rival, India. New Delhi, too, is trying to garner favor with the Afghans, and both Pakistan and India accuse each other of funding militant groups to destabilize their countries, with Afghanistan often the stage for the strikes.
Karzai said he is determined to prevent Afghan soil from being used by any countries to carry out attacks against each other.
"The bottom line here is that Afghanistan does not want any proxy wars on its territory," Karzai said.
Karzai met Wednesday with Pakistani President Asif Ali Zardari and has also visited army chief Gen. Ashfaq Parvez Kayani.