In meetings with Pakistani army chief General Ashfaq Kayani, Allen is expected to discuss militants operating from havens inside Pakistan, Islamabad's continuing blockade of Nato supply convoys to Afghanistan and other issues, said US officials, who spoke on condition of anonymity.
The United States withdrew its negotiating team from Pakistan earlier this month after talks stalled on the reopening of crucial routes into Afghanistan for Nato trucks.
US Defense Secretary Leon Panetta also has warned the United States is running out of patience over Islamabad's failure to crack down on Haqqani fighters staging cross-border attacks out of Pakistan.
Pakistan shut its borders to Nato supply convoys in November after 24 Pakistani soldiers were killed in a botched US air strike along the border.
Washington has expressed condolences but refused a demand from Pakistan to issue an apology over the incident.
The US military now runs supplies by air and over longer, more costly road and rail routes through Central Asia, the Caucasus and Russia.
Allen's visit coincides with political turmoil in Pakistan, after judges ousted the premier. Last week, MPs elected Raja Pervaiz Ashraf as Pakistan's new prime minister in a bid to end the crisis.
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