She was speaking in Beijing after two days of talks ahead of a planned visit by Pakistan's President Asif Ali Zardari next week to Xinjiang, the restive west Chinese region where members of the Uighur minority have mounted attacks.
Pakistan has leaned closer to China after its already tense relationship with the United States, its major donor, was further strained in May when US forces killed Osama bin Laden in Pakistan where he appears to have hid for several years.
Yet China has its own concerns over Pakistan. Officials in Kashgar, a city in south Xinjiang, said a stabbing attack there in late July was orchestrated by members of the separatist "East Turkestan Islamic Movement" (ETIM) who trained in Pakistan before returning to China.
Khar said, however, there were no rifts between Islamabad and Beijing over fighting militants, and cast doubt on the reports about a Pakistan link to the Kashgar attack.
"The statement vis-à-vis Pakistan's involvement of any sort was misconstrued, was not from the Chinese government," she told a news conference, referring to the Kashgar attack.
"Does it (ETIM) have any base in Pakistan? We don't know," she said, adding that her government would cooperate with China to eradicate such threats.
"We have a wide history of cooperating with the Chinese people to be able to dismantle this group or its presence in any form," she said.
China and Pakistan call each other "all-weather friends," their ties underpinned by shared wariness of their common neighbor, India, and a desire to balance US influence. The Pakistani minister's comments underscored their determination to set aside any potential public discord.
Khar said security issues brought Islamabad and Beijing closer together, rather than driving them apart.
"We respond to that (issue) by increasing our cooperation in counter-terrorism, increasing our intelligence cooperation," she added. "We need to make this even more robust."
Xinjiang sits next to south and central Asia, and China sees it as a vital bulwark in this volatile part of the world, making it all the more jumpy about unrest there.
Uighurs are a Turkic-speaking Muslims who form a minority in Xinjiang, and are culturally closer to ethnic groups across central Asia and Turkey than the Han Chinese who make up the vast majority of China's population.
Many resent the Han Chinese presence in their homeland.
But few experts see the ETIM group as capable of striking in Xinjiang. Rahimullah Yusufzai, a Pakistani expert, earlier told Reuters that officials told him there were only between 30 and 80 Uighur militants in Pakistan's tribal areas.
There is even uncertainty about whether the ETIM still operates as an effective organization. After a key leader of the group was killed in 2003, its activities went into decline.
China's Foreign Ministry has also praised Pakistan as a firm partner against terror and extremism, playing down the risk that ties could be strained by the attack. It did not mention any link to the Kashgar attack.
The assailants in Kashgar stormed a restaurant, set in on fire after killing the owner and a waiter, and then ran onto the street and hacked to death four people.
Pakistan's ambassador to Beijing, Masood Khan, told Reuters that Zardari will visit Xinjiang's regional capital, Urumqi, next week to attend the China-Eurasia trade fair.
Khar, in her mid-thirties, was appointed to foreign minister in July and is Pakistan's youngest ever holder of that job.