Addressing a joint press conference with Prime Minister Yousuf Raza Gilani on Thursday, Karzai underlined the importance of working together.
According to some analysts, Karzai's main mission of the Islamabad visit was to seek Pakistani help in promoting conciliatory gestures and peace efforts toward the Taliban, and according to them the recent action against top extremists leaders in Pakistan has not helped Kabul's cause.
Ahmed Rashid, a Pakistani journalist and expert on the Taliban who met with Karzai prior to his meeting with top Pakistani officials on Thursday said the arrests of Taliban leaders in Pakistan were a source of "a very serious underlying tension" between the countries.
Rashid said Kabul has been asking Islamabad to hand over Mullah Barader, who is second only to Taliban warlord Mullah Omar, but the demands have so far gone unfulfilled.
'There was a suggestion from the Afghan side that the Pakistani arrests of Taliban leaders were not helping Kabul. The word undermining Kabul's own initiative was used, and I think these tensions would have been a key in the talks with Prime Minister Gilani, as well as the Afghan and Pakistani intelligence chiefs,' The New York Times quoted Rashid, as saying.
'Some of the more pragmatic Taliban have been arrested by the ISI, and this has caused consternation in Kabul because these were the same people who were holding secret talks with the Kabul administration, and the other suggestion is that a number of hard-liners will replace Mullah Baradar and those arrested,' he added.
Rashid also pointed out that while Afghanistan has some issues over Pakistan's action, India, on the other hand, is uncomfortable with Islamabad's new strategy.
'India, of course, I think has got quite a fit that Pakistan is muscling in by making these arrests. There is an enormous amount of complexity and tension between all the major players right now in Afghanistan,' he said.
We are determined to help Afghanistan: PM
PML-N opposes operation against Taliban
Indian tabla player killed in Kabul attack
Kabul attack not targeted at Indians: Holbrooke
Taliban suspected behind kidnap of British boy