WASHINGTON — A US military investigation has concluded that it took about 90 minutes for Nato officers to notify a senior allied commander about Pakistan’s calls that its outposts were under attack, underscoring a lack of timely senior-level “override” measures to avoid deadly cross-border errors like last month’s airstrikes that killed 26 Pakistani soldiers.

Once alerted, the commander immediately halted American attacks on two Pakistani border posts. But by then, military communications between the two sides had sorted out a chain of errors and the shooting had already stopped. The delays — by two different officers — raise questions about whether a faster response could have spared the lives of some Pakistani soldiers.

An unclassified version of the report, released Monday by the military’s Central Command on its Web site, also revealed for the first time that an American AC-130 gunship flew two miles into Pakistani territory to return fire on Pakistani troops that had attacked a joint American-Afghan ground patrol just across the border in Afghanistan.

The 30-page report, which expanded upon a phone briefing last week by the chief investigator, Brigadier Gen. Stephen A. Clark of the Air Force, also found that competing Nato and American rules of engagement related to border-area and cross-border operations “lacked clarity and precision, and were not followed.”  The full report alters and expands upon the impression of the inquiry’s findings created by General Clark’s briefing, which had stressed how checks and balances on both sides failed. The report, for the first time, portrays unexplained delays and a lack of urgency by Nato officers in notifying their superiors of the unfolding late-night debacle that plunged relations between the two countries to new lows.

The report recommended nine changes, including reviewing and harmonizing all directives related to “near-border operations,” increased training and coordination, improved surveillance before missions, and up-to-date understanding of the location of border installations on both sides of the boundary separating the two countries.  Most of all, General Clark said, the two countries must take steps toward resolving the deep mistrust that prevented troops on both sides from sharing vital information about their locations and operations that could well have averted the tragedy.  “The way to long-term peace and stability along the border is to be found in resolving the longstanding border disputes that perpetuate a state of uncertainty and mistrust,” General Clark wrote.

The episode, the worst in nearly a decade riddled with fatal cross-border blunders, underscored gaping flaws in a system established in recent years to avoid such mistakes. American officials acknowledged that the policy of not divulging to Pakistan the precise location of allied ground troops in Afghanistan — for fear Pakistan might jeopardize their operations — contributed to the accident.

On Nov. 25, the same day the episode began, Gen. John Allen, the allied commander in Afghanistan, met in Islamabad with Gen. Ashfaq Parvez Kayani, the Pakistani Army chief, to try to improve border coordination procedures.

Pakistan has insisted that its forces did nothing wrong, and that they did not fire the first shots. Rather, senior Pakistani military and civilian officials have accused the United States of intentionally striking the border posts, even after Pakistani officers called their counterparts to complain that their outposts were under allied attack.

American officials said the first allied mistake was that NATO had not informed Pakistan about the patrol, so the Pakistani soldiers would not have known to expect allied forces nearby. NATO and Pakistani forces are supposed to inform each other about operations on the border precisely to avoid this kind of mistake.

But the report conclude that the Pakistanis fired first at the joint Afghan-American patrol of 120 soldiers and that they kept firing even after the Americans tried to warn them that they were shooting at allied troops.

Why the Pakistanis were firing remained unclear. Pakistan refused to participate in the inquiry, saying that American inquiries into previous cross-border mishaps were biased.