That means 4,000 agency employees will continue to be out of work until at least Labor Day.
Congress began its August recess Tuesday night.
Republicans and Democrats remain divided over a program that subsidizes commercial air service to rural airports.
President Barack Obama implored Congress on Tuesday to settle the dispute before leaving town, calling the stalemate "another Washington-inflicted wound on America."
The partial FAA shutdown began last month.
It has idled hundreds of construction projects nationwide, including one at Los Angeles International Airport.
The agency is likely to lose out on more than $1 billion in airline ticket taxes.
The government already has lost more than $200 million since airlines are unable to collect taxes on ticket sales because the FAA's operating authority has expired.
Air traffic controllers and airplane inspectors are not affected.
The Associated Press contributed to this story.