General Mattis, head of US Central Command overseeing the wars in Afghanistan and the Middle East, was expected to meet Pakistan's army chief Ashfaq Kayani for a "regular, scheduled visit", the US embassy in Islamabad had said.
"It's not extraordinary... it's a military to military relationship," said embassy spokesman Alberto Rodriguez.
But the visit comes after a US report this week criticised the Pakistani military for failing to forge a clear and sustained path to beat insurgents holed up in the lawless regions bordering Afghanistan.
The United States has long urged Pakistan to do more to combat militants in the tribal belt, which it considers a global headquarters of al Qaeda, saying such efforts are vital to help end the nearly decade-long war in Afghanistan.
The semi-annual White House report to Congress, released Tuesday, noted a deterioration of the situation in the Federally Administered Tribal Areas, and said operations were not complemented by plans to "hold" and "build" the areas.
"As such there remains no clear path to defeating the insurgency in Pakistan, despite the unprecedented and sustained deployment of over 147,000 forces," the report said.
Mattis is the most senior US official to visit Islamabad since Pakistan released a CIA contractor who shot dead two men in Lahore in January.
The killings and Pakistan's subsequent seven-week detention of Raymond Davis sparked a major diplomatic crisis in the fragile relationship between Washington and Islamabad.
A Pakistani court eventually freed Raymond Davis following the payment of $2 million in blood money to the families of the dead men.
Pakistani-US tensions remain high over an ongoing covert US drone campaign in the border region, which fosters deep anti-Americanism within Pakistan.
A missile strike on March 17 that killed 39 people, civilians among them, led to rare public condemnation by Kayani of the unmanned drone campaign, which continues with the tacit consent of Islamabad.
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