In this photo released by Inter Services Public Relations, U.S. Chairman of the Joint Chiefs of Staff Adm. Mike Mullen, left, listens to Pakistan's chairman of the Joint Chiefs of Staff Committee, Gen. Khalid Shameem Wynne. (AP)

A visit to Pakistan by Washington’s top military official Wednesday appeared to reinforce rather than diminish the growing divisions between the two strategic partners, especially over U.S. drone missile strikes and Pakistan’s failure to pursue a major Afghan-led insurgent group based in its tribal region.

The U.S. Embassy in the capital, Islamabad, said in a statement that Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, repeatedly stressed during his visit Washington’s “long-term commitment to supporting Pakistan in its fight against violent extremists.”

But comments by other U.S. officials and by Mullen, who spoke to a Pakistani newspaper Wednesday and during a stopover in Afghanistan on Tuesday, made it clear that the two security establishments remain far apart on the issues of which insurgent groups represent a threat and what methods should be used to quell them.

The tense visit came amid a flurry of Pakistani efforts to improve relations with the United States while also demanding more respect for Pakistani sovereignty. Lt. Gen. Ahmed Shuja Pasha, chief of Pakistan’s major intelligence agency, visited Washington last week. The country’s senior diplomat, Foreign Secretary Salman Bashir, will follow later this week.

Mullen told Pakistan’s Dawn newspaper that U.S. officials are aware of the “long-standing relationship” between Pakistan’s Inter-Services Intelligence agency and the Haqqani network, an aggressive militant group that supports the Afghan Taliban. He said that the group is aiding and training “fighters that are killing Americans” and that Pakistan’s relations with Haqqani are “at the core” of the bilateral difficulties.

Pakistani military officials have denied coddling Haqqani or pursuing what critics call a policy of selective repression and appeasement of Islamic militants. They say they are reluctant to launch attacks against new groups only because they are already immersed in a protracted military campaign against the Pakistani Taliban.

Mullen met privately with Pakistan’s chief of army staff, Gen. Ashfaq Kayani, but no detailed statement was issued about their talks. The men have met frequently and are said to have a cordial relationship, but recent comments by both about the actions of each other’s governments have revealed growing exasperation.

Kayani has been especially vocal about the issue of CIA drone attacks on militant targets in his country’s northwestern border region. The attacks are highly controversial in Pakistan, and Kayani issued a rare public protest against a strike several weeks ago that Pakistani officials said killed up to 40 villagers at a meeting. CIA officials said the victims were Taliban supporters.

Pakistani officials have repeatedly asked the United States to cut back the drone campaign, share intelligence about its targets and turn over drone technology so they can carry out such attacks themselves. But U.S. officials say the unmanned missile strikes are a crucial weapon in the war against Islamic militants, especially those Pakistan refuses to pursue.

One U.S official in Islamabad, speaking on the condition of anonymity, told journalists Wednesday that the United States has no plans to stop the drone campaign, but that “how it goes forward” will be decided by discussions among U.S. and Pakistani military and intelligence officials.

Special correspondent Shaiq Hussain in Islamabad contributed to this report.