A top Central Intelligence Agency official traveled secretly to Islamabad this month to confront Pakistan’s most senior officials with new information about ties between the country’s powerful spy service and militants operating in Pakistan’s tribal areas, according to American military and intelligence officials. The CIA emissary presented evidence showing that members of the spy service had deepened their ties with some militant groups that were responsible for a surge of violence in Afghanistan, possibly including the suicide bombing this month of the Indian Embassy in Kabul, the officials said. The decision to confront Pakistan with what the officials described as a new CIA assessment of the spy service’s activities seemed to be the bluntest American warning to Pakistan since shortly after the Sept. 11 attacks about the ties between the spy service and Islamic militants.