Gen Petraeus (left) also met Pakistan army chief Gen Ashfaq Kayani
The US says a new supply path to Afghanistan has been agreed with Central Asian states and Russia as an option to the troubled Pakistan route.
US Central Command chief Gen David Petraeus made the announcement on a visit to Islamabad.
The route through the Khyber Pass has been closed several times in recent months after militants attacks.
Gen David Petraeus met President Asif Ali Zardari and other leading figures on his one-day trip.
Meanwhile, Pakistani security forces say they have killed 60 militants in the past 24 hours in an operation in the tribal agency of Mohmand near the Afghan border.
There is no independent confirmation of the casualty figures.
Gen Petraeus's visit came after a week-long tour of Central Asian states.
He said the Pakistan route had been flowing "generally freely" in recent weeks but that the US and Nato had sought "additional logistical routes from the north".
He added: "There have been agreements reached and there are transit lines now and transit agreements for commercial goods and services in particular that include several countries in the Central Asian states and also Russia."
The BBC's Barbara Plett in Islamabad says most of Nato's supplies are transported overland through Pakistan, but support for the Nato war effort in Afghanistan is unpopular in Pakistan and supply trucks have increasingly been attacked by local militants.
Raids on trucks supplying Afghanistan have been a major concern
She says reports from the meetings also suggest that Pakistan expressed concern about US missile strikes against suspected Taleban and al-Qaeda militants in its border region.
The attacks have been blamed for many civilian casualties.
Islamabad says this triggers public anger, which undermines its own counter-terrorism efforts.
Our correspondent says there has been no formal indication that this policy might change under the new US administration, although a senior official of Barack Obama's Democratic party has questioned whether the missile strikes are counterproductive.
At his press conference, Gen Petraeus said the US would continue to help Pakistan tackle terrorism and militancy in the tribal areas.
"It is clearly in the interest of all countries involved that Pakistan succeed in dealing with its internal problems," he said.
Pakistan's actions and arrests following the Mumbai (Bombay) attacks were also discussed.
The general said the US and the international community would continue to support Pakistan, but Pakistan must also put its house in order on the issue of militants.
Gen Petraeus is a key advocate of a major US troop surge in Afghanistan.
The US has said it is sending up to 30,000 new troops to Afghanistan this year to take on a resurgent Taleban. They will join 33,000 US and 32,000 other Nato troops already in the country.
This is Gen Petraeus's second visit to Pakistan since taking up his new position.
He was until recently commander of the US military in Iraq.
He was widely credited with improving security there through the "surge" plan, which saw nearly 30,000 US troops deployed to trouble spots.
However, Afghanistan's ambassador to the US, Said Jawad, recently said that a plan similar to the one in Iraq that formed local tribal groups to help combat the insurgency was "very risky".