Congress passed legislation creating NextGen in 2003, and directed the agency to accommodate all types of aircraft, including drones.
The program, which is not expected to be completed for at least another decade, is replacing radar and radio communications, technologies rooted in the early 20th century, with satellite-based navigation and digital communications.
The FAA has spent more than $5 billion on the complex program and is nearly finished installing hardware and software for several key systems. But the further it progresses, the more difficult it becomes to make changes.
Government and industry officials have long maintained that drones must meet the same rules that apply to manned aircraft if they are to share the sky. That is changing, however, said Chris Stephenson, who represents the National Air Traffic Controllers Association on several U.S. and international unmanned aircraft committees.
"It's becoming painfully apparent that in order to get (drones) in there, there is going to have to be a fair amount of accommodation, at least in the beginning," he said.
Michael Whitaker, the FAA's deputy administrator, acknowledged that drones "weren't really part of the equation when you go back to the origin of NextGen."
The NextGen plans for the next five years do not address how drones will fit into a system designed for planes with pilots on board, but the agency will have to consider whether to do that, Whitaker told a recent meeting of the NextGen Institute, a non-profit association sponsored by the FAA so that industry can assist with research.
Most of the initial demand to fly unmanned aircraft came from the departments of Defence and Homeland Security, which wanted to test military drones or use them to monitor U.S. borders.
Later, interest began to build around potential uses for smaller drones, especially by police departments, but also for those wanting to spray crops, monitor pipelines and inspect offshore oil platforms. These drones can weigh anywhere from a few pounds to several hundred.
More recently, commercial demand has soared — from wedding videographers and real estate agents to Amazon and Google, eyeing potential package deliveries.
The FAA bans commercial drone operations with a few, limited exceptions. That ban, however, is undermined almost daily by frustrated small drone operators.
Bolton, also addressing the institute, said the NextGen office is working closely with a drone research team at the FAA's technical centre in Atlantic City, New Jersey.
FAA officials are under pressure from Congress and industry to loosen restrictions on smaller drones. The agency is expected to propose safety rules in November for businesses that want to operate them.
Smaller drones are less an issue for NextGen because the FAA is expected to limit their altitudes to less than 400 feet (120 metres). Air traffic controllers generally don't separate aircraft at such low altitudes, except near airports.
But there is also concern about potential traffic and collisions with low-flying smaller drones. NASA researchers are working with the FAA and industry to develop an air traffic control system for aircraft flying at 500 feet (150 metres) or lower. There is no such system today except around airports.
Medium to large drones that are eventually expected fly in "Class A" airspace — over 18,000 feet, (5,500 metres) where they must be able to avoid collisions with other aircraft — are more of a problem for NextGen.
They will be controlled by a ground pilot, who will be able to see where the drone is on a computer screen and can communicate with controllers. But there won't be a pilot on board who can look out and adjust course to avoid a collision.
There are other differences as well.
Pilots who fly in Class A airspace file flight plans identifying their routes. But some larger drones are expected to stay aloft at high altitudes for days or weeks at a time, and their flight plans will be much more complex.
ERAM, a NextGen computer system that controllers use to guide high-altitude air traffic, won't be able to handle such voluminous flight plans and will have to be adjusted, aviation experts said. ERAM is already over budget and years overdue.