Pakistani officials have complained publicly about the attacks from unmanned US aircraft in the Tribal Areas bordering Afghanistan. It said that strikes like these are a violation of its sovereignty and will increase public resentment towards both Pakistan government and the United States.
US officials normally decline to comment publicly on reports of the missile strikes, but Gates made an exception when asked about Pakistan's complaints at a hearing of the Senate Armed Services Committee.
The reports in The Daily Times newspaper suggest that this was the first time that Gates has testified before Congress as Obama's Pentagon chief.
"Both President Bush and President Obama have made clear that we will go after al Qaeda wherever it is and we will continue to pursue that," Gates said.
Asked by committee chairman Senator Carl Levin, if that decision had been conveyed to the Pakistani Government, Gates replied: "Yes, sir."
He described the war in Afghanistan as the US military's greatest challenge and top priority under President Barack Obama.
"There is little doubt that our greatest military challenge right now is Afghanistan," he said. "President Obama has made it clear that the Afghanistan theatre should be our top overseas military priority."
Gates said US and NATO military operations that killed civilians caused 'enormous harm' to American interests in Afghanistan, and added a shortage of ground forces led to over-reliance on airstrikes.
"My worry is that the Afghans come to see us as part of the problem rather than part of the solution, and then we are lost," he warned. "We have got to figure out a better way to do these things."&13;&13;