Gates arrived in Pakistan on Thursday, urging the authorities to root out Afghan Taliban factions based in its northwestern border areas from where they have been orchestrating an intensifying battle in Afghanistan.
But Gates has been careful not to repeat the usual US call for Pakistan to "do more" in the battle against Taliban fighters, a demand that has infuriated Pakistan which has lost about 2,000 soldiers.
Islamabad has mounted big offensives against Pakistani Taliban factions attacking the state, but has resisted US pressure to go after Afghan Taliban fighters in border enclaves who do not strike in Pakistan but cross the border to fight US troops.
Gates commended the Pakistani military's success against fighters since early last year and also called for it to pressure Afghan factions.
"Only by pressuring these groups on both sides of the border will Afghanistan and Pakistan be able to rid themselves of this scourge," he said.
But Gates also stressed that it was up to Pakistan to decide on the timing of its action.
"The Pakistani leadership will make its own decisions about what the best timing for their military operations is, about when they are ready to do something or whether they are going to do it at all."
Many Pakistanis are deeply sceptical of the US military presence in the region believing it is aimed at suppressing Muslims. Many also believe the United States wants to confiscate its nuclear weapons.
Gates said "further worsening the situation is an organised propaganda campaign by the very groups we seek to destroy".
"So let me say, definitively, that the United States does not covet a single inch of Pakistani soil, we seek no military bases here, and we have no desire to control Pakistan's nuclear weapons."