The Federal Aviation Administration will miss a September 2015 deadline set by Congress to allow drones to fly throughout the nation’s skies because of technical and regulatory obstacles that are unlikely to be resolved anytime soon, according to a government audit released Monday.

The FAA is significantly behind schedule in drawing up rules and standards to ensure that drones are airworthy, that pilots are trained properly and that their aircraft won’t interfere with other air traffic, the Transportation Department’s inspector general concluded in a highly critical audit.

The report said the FAA has so many hurdles to confront that it is unclear when — or if — remotely controlled aircraft can be safely integrated into U.S. airspace.

In 2012, Congress passed a law that effectively legalized commercial and civilian drone flights in the United States. With backing from drone manufacturers and other businesses eager to embrace a new era in aviation, lawmakers directed the FAA to come up with rules and standards to permit widespread drone traffic by Sept. 30, 2015.

The inspector general’s audit, however, highlighted the difficulties of absorbing drones into U.S. skies and concluded that “safety risks will persist” until the FAA can establish a set of rules for doing so.

A Washington Post investigation in June found that at least 49 large military drones have crashed while on training missions in the United States since 2001. In addition, nearly two dozen civilian drones have been involved in accidents since 2009, according to FAA data. More recently, a rising number of small, unlicensed drones have flown dangerously close to passenger planes near some of the country’s busiest airports.

The FAA has missed several deadlines, much to the frustration of manufacturers and lawmakers eager to see drones used more widely. The inspector general’s audit found that many basic barriers remain and that “the magnitude of unresolved safety and privacy issues will prevent” the FAA from meeting the timetable imposed by Congress.

Les Dorr, an FAA spokesman, acknowledged that the agency faces numerous challenges but said it has made “significant progress” toward safely integrating drones into the nation’s airspace.

In an e-mailed statement, Dorr said the FAA agrees with the inspector general’s recommendations for improving the process. He said the agency plans to propose regulations governing the use of small drones — those that weigh less than 55 pounds and don’t fly above 400 feet in altitude — this year.

The FAA had said it would issue proposed rules for small drones three years ago. Transportation Department auditors said the delay was largely due to uncertainty over how and whether the rules should include privacy protections to prevent drone operators from conducting surveillance. Small drones are relatively cheap — some models cost about $500 — and can be equipped with powerful cameras.

After the FAA issues proposed rules for small drones this year, the agency must then allow for a lengthy period of public comment before finalizing the standards. The audit estimated that the rules wouldn’t become final until next year at the earliest. Standards for larger drones that would share airspace with passenger planes aren’t expected to be fixed for several more years.

The FAA has imposed a de facto ban on commercial drones until it can sort out the rules of the sky. The agency has issued only two permits for commercial operations, both of them in rural parts of Alaska. FAA officials have said they may relax restrictions in the coming months for a handful of industries, including filmmakers, oil-and-gas producers and large-scale farms.

Michael Toscano of the Association for Unmanned Vehicle Systems International talks to Nia-Malika Henderson about the effort to educate the public about unmanned aircraft systems, and to dispel the myths of “drones.” (Nicki Demarco/(On Background))

Because drones are inexpensive and relatively easy to operate, however, many users are flying them anyway — increasingly in an unsafe manner.

In 15 cases over the past two years, drones have flown dangerously close to passenger planes near airports, including two incidents on the same day in May in New York and Los Angeles, according to FAA reports obtained by The Post. A separate aviation safety database managed by NASA has recorded 50 other reports of close calls or improper flight operations involving drones over the past decade.

Although commercial drones are effectively banned for the moment, the FAA has issued about 300 special-use certificates for public agencies to fly the aircraft. About half of those have been granted to the military to train with drones in civilian airspace. Many others have been issued to law enforcement agencies, such as Customs and Border Protection, which flies large surveillance drones along the borders with Canada and Mexico.

The audit also blamed the delays on technological barriers that the FAA and manufacturers have been unable to resolve.

Drones rely on GPS signals to navigate and are controlled by pilots or operators on the ground via a two-way radio transmission link. But those links are not completely reliable, and it is common for operators to lose control of a drone for seconds or minutes at a time.

With no pilot in the cockpit, drones also lack the technology to see and avoid other aircraft, raising the risk of a midair collision. The inspector general called that problem the “most pressing technical challenge to integration.”

Manufacturers are hard at work on fixes to both of those technological shortcomings. But the audit indicated that solutions are not close at hand.