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WASHINGTON – Documented close calls between aircraft in U.S. skies shot upward last year as the government switched on more automatic monitors to track the incidents, a new report says.

Cases in which aircraft came closer together than U.S. Federal Aviation Administration rules allow rose to 4,394 in the year ending Sept. 30, 2012, from 1,895 the previous year, according to agency data released Thursday.

The increase indicates there have been many more close calls in U.S. aviation than the FAA knew about when it largely relied on humans to report errors.

Through better reporting, the agency can identify hazards more precisely and improve safety, according to the report.

“Collaboration is now the rule, not the exception,” David Grizzle, chief operating officer of the FAA’s Air Traffic Organization, said in the report. “We’ve gone from counting errors to identifying and mitigating safety risk.”

The most high-risk incidents, those that came closest to an accident such as a mid-air collision, declined as a percentage of total incidents.

This shows that risks in the system have declined, according to a presentation Thursday by Joseph Teixeira, vice president of the air traffic unit.

The results continue a trend of increasing air-traffic controller errors logged by the FAA since 2009, when the agency began a series of initiatives to discourage cover-ups and identify cases that weren’t being noticed.

In fiscal 2009, there were 1,234 errors connected to controllers who allowed planes to get too close. Near airports, planes usually must be separated by 3.5 miles or 1,000 feet of altitude.

The FAA has attributed the increase to an initiative that encourages controllers to report errors without fear of punishment.

The agency also stopped basing air-traffic managers’ raises in part on the number of controller errors reported at a facility.

“We are proud of the collaborative efforts we have undertaken with the FAA to reduce safety incidents and increase reporting opportunities for controllers and FAA employees,” Doug Church, a spokesman for the National Air Traffic Controllers Association, the union representing more than 15,000 controllers, said in an email statement.

At the same time, new technology at radar facilities monitoring air traffic near large airports has for the first time begun automatically identifying near-misses.

Close calls on runways also were up last year, according to the report.

Incidents that came closest to a collision between two planes, or a plane and ground equipment, totaled 18 last year, more than twice the seven that occurred in 2011.

The data released Thursday doesn’t clarify whether there are more air-safety incidents or just better reporting of what was previously occurring.

In addition to switching on automatic reporting at all FAA air-traffic facilities, the agency changed some of its definitions for counting incidents, making it difficult to compare against data from previous years.