His comments followed remarks by Admiral Mike Mullen, the Chairman of the US Joint Chiefs of Staff, accusing Pakistan's Inter-Services Intelligence (ISI) agency of having ties with militants in the northwest tribal belt.
The army chief "strongly rejected negative propaganda of Pakistan not doing enough and Pakistan army’s lack of clarity on the way forward," the military said in a statement, a day after Mullen met top military generals in Islamabad.
Kayani said that the "army’s ongoing operations are a testimony of our national resolve to defeat terrorism", according to the statement.
In an interview with TV channel Geo, Mullen -- the highest ranking officer in the US armed forces -- said: "ISI has a long standing relationship with the Haqqani network, that does not mean everybody in ISI but it is there."
But the military statement said Mullen "lauded the sacrifices and efforts of people of Pakistan and its security forces" in the war against terror.
He also made reassurances that "security ties will not be allowed to unravel between the two armed forces".
The Haqqani network is an al Qaeda-allied organisation run by Afghan warlord Sirajuddin Haqqani and based in the North Waziristan tribal district.
The group has been blamed for some of the deadliest anti-US attacks in Afghanistan.
Kayani and Mullen re-stated their aims of building "reciprocal respect towards each other’s sovereignty" and addressing the "trust deficit between the institutions as well as the people on both the sides," the statement said.
Kayani described public support as the key to success in the war against terrorism but said that controversial US drone strikes "not only undermine our national effort against terrorism but also turn public support against our efforts".
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