Thousands of civilians - overwhelmingly Muslim - continue to be slaughtered in extremist attacks, contributing to the instability of the often shaky, poverty-stricken governments in the region, the statistics compiled by the National Counterterrorism Center show.
The struggling nations provide havens for terrorists who are increasingly targeting the U.S. and other Western nations. At the same time, U.S.-led operations against insurgents increased in both countries.
"The numbers, to a certain extent, are a reflection of where the enemy is re-gathering," said Juan Zarate, a top counterterrorism official in the Bush administration who is now senior adviser at the Center for Strategic and International Studies.
"So, to the extent we are seeing more attacks in Afghanistan and Pakistan, it's a reflection of resistance to U.S. policy and presence as well as a strategic shift by groups like al Qaeda and foreign jihadis to concentrate where they think they will be most effective," he said.
U.S. intelligence officials said the 2009 totals - they do not include attacks on the military - offered one glimmer of hope: Terror attacks in Pakistan were growing substantially early in 2009 but leveled out toward the end of the year as Pakistani forces stepped up their assaults on militant strongholds along the border.
CBSNews.com Special Report: Afghanistan
The rise in violence in South Asia was offset by a continued decline in attacks in Iraq, leading to an overall decrease in terrorism worldwide in 2009, compared with 2008. In Iraq, the number of attacks fell by nearly a third from 2008 to 2009, and suicide bombings have plunged from more than 350 in 2007 to about 80 last year.
But even beyond South Asia, the overall picture of terrorism last year underscored new threats in Somalia and Yemen, where insurgents have gained strongholds in vast lawless stretches.
The terror threat to the United States is partly a function of the level of violence worldwide, said Bernard Finel, a senior fellow with the American Security Project.
"The larger the pool of extremists, the larger the risk that some will choose to attack American interests or be recruited into groups like al Qaeda with global aspirations," he said.
While there are varied reasons for the terror trends, they partly reflect policy decisions by the Bush and Obama administrations to pull out of the gradually improving situation in Iraq and focus military and diplomatic efforts on Afghanistan and Pakistan.
The increased military pressure in Pakistan, experts say, has helped disrupt al Qaeda and Taliban groups. But in Afghanistan, it has fueled the insurgency, spawning increased attacks against citizens in what experts suggest is an insurgent campaign to destabilize the government and generate militant recruits.
The National Counterterrorism Center statistics measure attacks against civilians. They will be released later this week in conjunction with the State Department's annual assessment of global terrorism.
U.S. officials spoke about the trends on condition of anonymity in advance of the public release.
The numbers show that nearly 7,000 civilians were killed and injured in Afghanistan terror attacks last year, a 44 percent increase over 2008. In Pakistan, more than 8,600 were killed and wounded last year, a 30 percent jump.
According to the officials, Pakistan's push into the Federally Administered Tribal Areas and the Swat Valley put more pressure on the insurgents toward the end of the year, tamping down militant activity and forcing them to relocate.
At the same time, the U.S. also targeted the border region by dramatically increasing its classified program of drone attacks, largely conducted by the CIA. As a result, the officials said, the overall increase in Pakistan violence was less than initially expected during the more turbulent first half of the year.
"The military pressure has dislodged the (terror) groups from some of their training areas and kept them on the run," said Finel, who has just completed his own review of terror incidents and provided a preview of his results.
He said Islamist violence fell by 60 percent in the last half of 2009, compared with the first half. But he cautioned that the impact of the military action may not last, and terror groups are likely to rebound if the root of their extremist ideologies lives on.
Overall, the number of terror attacks in Pakistan rose from about 1,800 in 2008 to more than 1,900 attacks in 2009. Suicide bombings more than doubled between 2007 and 2009, jumping from 40 to 84.
In Afghanistan, attacks increased from more than 1,200 in 2008 to about 2,100 in 2009. Officials warned that the 2008 numbers may be a bit understated because of the difficulties in obtaining accurate reports from the war zone.
Last year, the U.S. began pouring troops into the foundering Afghan war and more forces continue to move in this year, bolstering a gradually unfolding offensive into the southern region.