Foreign affairs adviser Sartaj Aziz is the most senior member of Pakistan's new government to visit Afghanistan and is expected to meet Karzai later today.
The new administration took office last month after Prime Minister Nawaz Sharif won historic elections, at a time when relations between Kabul and Islamabad are even frostier than normal.
"I have brought a message of cordiality and goodwill for Afghanistan," Aziz told a news conference.
International efforts to start talks with Taliban insurgents on ending 12 years of war are in disarray after the disastrous opening of a Taliban liaison office in Qatar last month.
The office was initially hailed as a first step towards a peace deal, but a furious Karzai slammed it as an unofficial embassy for a Taliban government-in-exile.
The scheduled departure next year of around 100,000 US-led foreign troops and Afghan presidential elections in April have lent renewed urgency to the quest for peace.
The West considers Pakistan's support vital to achieving lasting peace with the Taliban in Afghanistan. But relations between the neighbours are mired in mutual distrust and accusations over Taliban and other Islamist militancy which plagues both countries.
"For us, a peaceful, stable and united Afghanistan is in the interest of Pakistan," said Aziz, calling for a "close relationship" and reiterating Islamabad's support for an "Afghan-led" peace process with the Taliban.
Sharif has kept Pakistan's foreign affairs portfolio under his own control but Aziz, who served as a minister in the 1990s, is effectively the foreign minister.
Aziz denied perceptions held by many in Afghanistan that Pakistan controls the Taliban, given that its leaders have presumed sanctuary in Pakistan, and insisted Islamabad could only help bring about a deal and not impose one.
"We have some contacts with the Taliban because of the past but we don't control them," he told the news conference.
In an unusually blunt remark, Afghan Foreign Minister Zalmai Rassoul said that efforts on both sides to strengthen relations, fight terrorism and ignite peace talks "have not been successful". "I hope the new government of Pakistan will open a new chapter in Pakistan-Afghan relations," he told the same press conference.
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