FAA Air Transportation Modernization and Safety Improvement Act - Authorizes appropriations for FY2010 and FY2011 for: (1) Federal Aviation Administration (FAA) operations; (2)FAA air navigation facilities and equipment; (3) civil aviation research and development (R&D); (4) airport planning and development and noise compatibility planning programs; (5) certain other aviation programs; and (6) administrative expenses for certain airport programs.

Revises procedural requirements for imposition of aircraft passenger facility charges (PFCs). Establishes an alternative PFC collection pilot program.

Revises the federal share of costs for certain airport improvement projects.

Directs the Secretary of Transportation to establish a pilot program for up to three states to participate in the airport improvement program (AIP) state block grant program.

Directs the Secretary to establish a pilot program to carry out up to six environmental mitigation demonstration projects at public-use airports.

Establishes: (1) an Air Traffic Control Modernization Oversight Board; and (2) the position of Chief NextGen Officer who shall implement all Next Generation Air Transportation System (NextGen) programs of the Department of Transportation (DOT).

Requires the FAA Administrator to: (1) consider whether the provision of NextGen air traffic services by nongovernment providers would promote safety and improve efficiency of the National Airspace System; and (2) make recommendations for the realignment of FAA services and facilities to assist in the transition to next generation facilities.

Revises FAA personnel management system requirements with respect to the mediation, alternative resolution, and binding arbitration of disputes between the FAA Administrator andFAA employees about implementation of proposed changes to the system.

Requires the FAA Administrator to report on navigation performance and area navigation operations and procedures required to maximize the efficiency and capacity of NextGen commercial operations at 35 Operational Evolution Partnership (OEP) airports.

Requires the FAA Administrator to report to Congress on the program and schedule for integrating automatic dependent surveillance-broadcast (ADS-B) technology into the national airspace system.

Requires the FAA Administrator to develop a plan to accelerate the integration of unmanned aerial systems into the National Airspace System.

Establishes the FAA Task Force on Air Traffic Control Facility Conditions.

Authorizes the Secretary to enter into cooperative agreements with up to five states to establish state ADS-B equipage banks.

Requires air carriers and airport operators to propose for the Secretary's approval contingency plans for passenger service during grounded aircraft flight delays.

Directs the Secretary to establish in the DOT: (1) a consumer hotline telephone number for air passenger complaints; and (2) an advisory committee for aviation consumer protection.

Revises requirements and increases additional funding for the Essential Air Service program.

Extends the small community air service development program through FY2011.

Directs the FAA Administrator to issue a plan to develop a schedule for installation of systems to alert controllers and flight crews to potential runway incursions.

Authorizes the FAA Administrator to access the criminal history records or databases systems of specified federal law enforcement agencies.

Requires helicopter and fixed-wing aircraft certificate holders providing emergency medical services to comply with federal safety operating requirements if there is a medical crew on board, without regard to whether patients are also on board.

Directs the FAA Administrator to: (1) establish within the FAA a national review team to conduct periodic, random reviews of FAA's oversight of air carriers; (2) conduct a review and evaluation of the FAA's Academy and facility training programs; and (3) develop a plan for the reduction of runway incursions.

Establishes in the FAA an Aviation Safety Whistleblower Investigation Office.

Directs the FAA Administrator to establish and implement a safety assessment system for foreign repair stations that perform maintenance on U.S. aircraft.

Directs the FAA Administrator to establish and maintain a pilot employment, training, and testing database.

Requires the FAA Administrator to: (1) develop and implement a plan for reevaluation of flight crew training, testing, and certification regulations; (2) issue a final rule to establish safety standards for training programs for flight crew members and aircraft dispatchers; and (3) establish research grant programs to reduce civilian aircraft noise and emissions and to develop jet fuel from clean coal.

Reauthorizes through FY2012 the FAA Center for Excellence for Applied Research and Training in the Use of Advanced Materials in Transport Aircraft.

Extends the Secretary's authority to provide insurance and reinsurance against loss or damage arising out of any risk from the operation of a domestic or foreign aircraft.

Prohibits operating certain aircraft weighing 75,000 pounds or less that do not comply with stage 3 noise levels.

Directs the FAA Administrator to: (1) establish a pilot program for redevelopment of airport properties; and (2) initiate a study on front line manager staffing requirements for FAA air traffic control facilities.