WASHINGTON (CNN) - Defense Secretary Robert Gates opened his first comments to Congress as President Barack Obama's defense secretary Tuesday with the clear message that Afghanistan is at the top of his to-do list.
"There is little doubt that our greatest military challenge right now is Afghanistan," Gates said in his opening statement before the Senate Armed Services Committee, adding that Obama has made it the top military priority overseas.
Watch the testimony on CNN.com/live
Later, in response to a question from the committee's chairman, Sen. Carl Levin, D-Connecticut, he said missile strikes in Pakistan will continue in an effort to root out al Qaeda members who have based themselves across the border from Afghanistan.
And in one of the clearest indications of the military's planning to add troops in Afghanistan, Gates outlined a deployment of two brigades by spring and a third by late summer.
Additional troops, even if available to deploy, could not be added until later this year because it would take that much time to build out the required infrastructure in Afghanistan to support the troops, he added.
Sen. John McCain, R-Arizona, who was instrumental in pushing for a troop surge in Iraq, warned that a troop increase in Afghanistan may not achieve the same results.
Gates himself noted that increased military presence must be accompanied by non-military solutions if progress is to be made in the war.
"While this will undoubtedly be a long and difficult fight, we can attain what I believe should be among our strategic objectives: an Afghan people who do not provide a safe haven for al Qaeda, reject the rule of the Taliban, and support the legitimate government that they elected and in which they have a stake," Gates said.
On missile strikes in Pakistan, Gates said that "both President Bush and President Obama have made clear that we will go after al Qaeda wherever al Qaeda is. And we will continue to pursue this."
Asked by Levin if Pakistan is aware of this continued pursuit, Gates replied simply, "Yes, sir."
Regarding withdrawal from Iraq, Gates said the military is planning various options, with the quickest withdrawal being the 16-month period - ending in May 2010 - outlined by Obama when he was running for president.
"We are working on a range of options for the president," he said. Among them is "essentially a completion of the work of the brigade combat teams and a transition to an assist-and-advisory role beginning at 16 months and proceeding further forward."
Under a recently approved agreement with the government of Iraq, the United States is required to have all troops out of that nation by the end of 2011. Even after that, however, Gates indicated a continued role of some kind is likely.
"As our military presence decreases over time, we should still expect to be involved in Iraq on some level for many years to come - assuming a sovereign Iraq continues to seek our partnership," he said. "The stability of Iraq remains critical to the future of the Middle East, a region that multiple presidents of both political parties have considered vital to the national security of the United States."
Gates also acknowledged that some decisions he had decided to put off when he was Bush's defense secretary are now back on his plate, especially the budget.
"As I focused on the wars these past two years, I ended up punting a number of procurement decisions that I believed would be more appropriately handled by my successor and a new administration. Well, as luck would have it, I am now the receiver of those punts - and in this game there are no fair catches," Gates noted.