Date: 201605
Local time of day: 0001-0600
Location: ONT.Airport, CA
Aircraft: Medium Transport
Flight plan: IFR
Flight phase: Taxi
Airspace: Class C ONT
ATC / advisory: Tower ONT
Reporter organization: Government
Reporter function: Other / Unknown
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Communication Breakdown; Situational Awareness; Distraction
Second reporter function: Other / Unknown
Anomaly: ATC Issue All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy; Inflight Event / Encounter Weather / Turbulence
Detector: Person Air Traffic Control
Contributing factors: Environment - Non Weather Related; Human Factors; Staffing; Weather; Procedure
Primary problem: Weather

Narrative: At the time of the event we were experiencing thunderstorms; lightning; hail; flooding in the cab; delays and flight plan timeouts. We were also short staffed as a result of a sickout and a controller performing an extra duty. We also had a tech ops employee in the cab patching multiple leaks in the ceiling during the incident.The Ground Controller verified coordination on a departure with SCT who coordinated a time and reiterated the altitude (maintain 4;000). The ground controller relayed this to the Tower Controller; who misheard the 4;000 and thought he heard 5;000.The environmental factors were an overwhelming factor in this scenario (weather; cab flooding; staffing; confusion); but the one thing that might have prevented the mis-issued altitude was the reiterated altitude assignment. Since 4;000 is part of the LOA there could be (and was) potential confusion.


Second narrative: Aircraft X was holding short of Runway 26L for IFR departure. SCT Traffic Management Unit (TMU) called back with a flow void time. If Aircraft X did not depart by then; they would have to hold for a lengthy delay. The strip was delivered to Local Controller and told that Aircraft X is void at [time]. Local Control was advising an aircraft on final of the weather conditions at the airport. I flashed Aircraft X in the rundown list to SCT POM Sector for the release and called them to let them know that Aircraft X was also Amendment 1 for final altitude. The SCT controller advised to have Aircraft X to maintain 4;000 feet; which was already the assigned altitude. Thunderstorm and heavy rain with small hail was present.A miscommunication must have taken place as the Local Controller told Aircraft X to maintain 5;000 feet when he was only assigned 4;000 feet as a final altitude. Also we had a large leak coming in from the roof of the Tower Cab with lots of water running in at the time. Tech Ops was over trying to work on funneling the leaking water into a contraption made of a tarp and a trash can to help collect the running water. This was a big distraction in the tower for over 3 hours including during this incident.The large leak with lots of water coming into the Tower Cab and Tech Ops working on stopping it caused a big distraction. It was a onetime thing; but we need repairs here.


Synopsis: ONT Tower controllers reported of a miscommunication relating to a clearance. Aircraft departing was restricted to 4;000 feet; the Controller mistakenly heard then issued 5;000. Distractions were reportedly involved.