Taliban fighters have stepped up attacks from Pakistan into Afghanistan and are taking advantage of a deal between the Pakistani government and local tribes that was billed as an effort to reduce the threat, US military officials said on Tuesday.
US officials also say the commanders of Afghanistan's Taliban insurgency reside in Pakistan.
The Taliban were resurgent in 2006, increasing attacks on NATO troops and Afghan government forces.
"Our military relations, our dialogue between Afghanistan, NATO, the United States and Pakistan is good but I'd also emphasise that we do have a challenge right now with command and control of the Taliban forces that has to be addressed," said Lieutenant General Karl Eikenberry, the top US commander in Afghanistan.
US Defence Secretary Robert Gates began a visit to Afghanistan on Monday, aiming to ensure military commanders have the resources to counter an expected spring offensive by the Taliban.
"The enemy does use both sides of the border, they use the inside of Pakistan as well for command and control," Eikenberry told reporters travelling with Gates.
"And they have senior leaders that operate on both sides."
Pakistan sealed an agreement in early September with tribes in the area of North Waziristan under which Pakistani troops would withdraw to garrisons on the understanding the tribes would not tolerate incursions into Afghanistan.
Eikenberry said the number of cross-border attacks in that area last month was 200 percent higher than the same period a year ago. He did not give precise figures.
Colonel Tom Collins, a spokesman for US forces in Afghanistan, said there were signs the deal with the tribes had worsened the situation.
"We're seeing evidence that the enemy is taking advantage of that agreement to launch attacks into Afghanistan," he told reporters.
Eikenberry said the porous border with Pakistan, where members of the same tribes live on both sides, was a long-term problem which would take time to solve.
US military officials also say they have hard evidence of Taliban fighters crossing the border unimpeded close to Pakistani border checkpoints.
"The safe haven that Pakistan presents cannot be over-emphasised," said a US military intelligence official, speaking on condition of anonymity.
"Command and control resides in Pakistan while operations occur in Afghanistan," the official said.
"Training, financing, recruitment, indoctrination, regeneration and other support activities occur in Pakistan."
Last year was Afghanistan's bloodiest since U.S.-led forces toppled the Taliban government in 2001 in response to the Sept 11 attacks. More than 4,000 people died in the violence.
Bomb attacks jumped from 783 in 2005 to 1,677 last year and suicide attacks surged from 27 to 139, according to US military figures.
Eikenberry said he expected the Taliban to try to increase violence in southern Afghanistan in the spring but NATO and US forces were already taking steps to meet the threat.
Fighting in Afghanistan often subsides during winter only to increase again after the snows melt.
"Although it's going to be a violent spring and I would expect that we'll have more violence into the summer, I'm absolutely confident that we're going to be able to dominate," Eikenberry said.
Eikenberry said he did not anticipate any reduction this year in the approximately 23,000 US troops in Afghanistan.
About half of them serve as part of a NATO force while the rest conduct missions ranging from training to counter-terrorism.