Date: 201407
Local time of day: 1201-1800
Location: BOI.Airport, ID
Light: Daylight
Aircraft: Military
Operator: Military
Operating under: Part 91
Flight plan: IFR
Mission: Tactical
Flight phase: Takeoff / Launch
Airspace: Class C BOI
ATC / advisory: Tower BOI
Second aircraft: Medium Large Transport
Reporter organization: Government
Reporter function: Local
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Communication Breakdown; Situational Awareness
Second reporter function: Flight Data / Clearance Delivery
Anomaly: Conflict Ground Conflict; Critical; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance; Ground Incursion Runway
Result: Flight Crew Took Evasive Action
Contributing factors: Airport; Procedure
Primary problem: Airport

Narrative: While working Local Control; I had 1 aircraft doing touch and goes in the pattern; which wasn't a factor in the situation. Aircraft X had been cleared for takeoff on 10R and switched to Departure frequency on the ground as required by 7110.65. Ground Control had coordinated to cross Runway 10R with Aircraft Y at the midfield Echo taxiway after Aircraft X departed. I approved this as Ground currently cannot taxi any aircraft to the active runway when we are on an east flown due to airport construction and them closing the parallel runway for even taxiing aircraft even though there is no construction on the runway and no safety risks on the runway. As all the construction is on the parallel taxiway; which forces us to have to cross the active runway multiple times through out a shift. Because of this Aircraft Y needed to cross. The Aircraft X [type] typically do a 30-45 second hold in position to do a systems check [to] run their engines up. While Aircraft X was doing this I was scanning the departure corridor to make sure there was no traffic; and then scanning to check on my Cessna who was in the downwind. As I was in the process of this scan Ground alerted me to Aircraft Y crossing the hold line; I immediately went to talk [to] Aircraft X and stop his takeoff roll but he had already started to roll and was no longer on my frequency without having a departure override I was unable to cancel Aircraft X's takeoff clearance or at least alert him to the traffic entering the runway. Aircraft Y; after penetrating the runway environment; turned sharply to the right to attempt to avoid and minimize any potential collision. Aircraft X was able to pull the aircraft into the air at a speed and location that was well before the normal rotation point for the Aircraft X [type]. While the collision was averted the aircraft came with in 50-100 feet of each other. Aircraft X then came back on frequency and made sure I was aware of the Aircraft Y on the runway.I have two recommendations to help in a future situation like this: 1. The airport needs to plan and consult with ATC to have minimal impact on taxi routing and minimal runway crossing. Through out this summer runway construction the airport has for the most part said here is what we are doing and; you need to work around us. In the past they worked well with us; but for the last few years they will no longer consult us since they have employed new people in the Management ranks; who refuse to work well with us. This has caused numerous incidents that could have been avoided if they would work with us. This event is just the culmination of their refusal to consult and work with us to minimize potential risks and inconvenience to the user. If they would open the closed runway to allow us to taxi on it during daylight hours which happen to be our busiest we would no longer have to cross the active runway.2. If at all possible the facility needs to install a Departure Control override button that allows the Local position instantaneous communication with any aircraft that has been switched to Departure on the ground. I'm not certain if our current communication gear will allow that; but I know we had this feature in the military and it saved situations like this from happening a few times. If we are unable to program in this feature then we need to sign a letter of agreement with the [military] that they will monitor the Local/emergency frequency as well as the Radar Frequency until they are airborne. That way we can cancel or abort their takeoff if we have a safety risk.


Second narrative: I was on Clearance Delivery and CIC combined.  Was alerted to the situation by the Local Controller.  I observed Aircraft Y stopping on the white line of Runway 10R after being instructed by Ground Control to hold short of runway.  Aircraft X did appear to lift off early and with expedited climb and passed through the intersection of Runway 10R and E at approximately 50 feet AGL.BOI airport is under construction and has numerous taxiways and runways closed during this time.  The number of crossings of the active runway went from less than 10 per day to well over 100 per day because of the airport's refusal to adjust the project.  Runway 10L was not being reconstructed and remains closed. Opening the runway for taxiing aircraft would prevent all but the normal 10 per day crossings of the active runway.  This shear number of crossings drastically increases the likelihood of runway incursions.  Convince the airport to open runway 10L for taxiing aircraft!Although the taxi instructions were complete; including the instructions to hold short of Runway 10R; the Ground Controller failed to hear a complete read back of taxi instructions which did not include a hold short of runway.


Synopsis: Two BOI Tower Controllers report of a runway incursion that caused a departure to leave the runway earlier than normal.  The Controller couldn't cancel the takeoff clearance because the military aircraft had already changed to Departure frequency as required.