Date: 201705
Local time of day: 0601-1200
Location: PAO.Tower, CA
Flight conditions: IMC
Light: Daylight
Aircraft: Small Aircraft; Low Wing; 1 Eng; Retractable Gear
Operator: Personal
Operating under: Part 91
Flight plan: IFR
Mission: Personal
Flight phase: Final Approach
Airspace: Class D NUQ
ATC / advisory: Tower PAO
Second aircraft: Military Transport
Reporter organization: Government
Reporter function: Local
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Human-Machine Interface; Communication Breakdown; Situational Awareness
Anomaly: ATC Issue All Types; Conflict Airborne Conflict; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Detector: Automation Air Traffic Control
When detected: In-flight
Contributing factors: Procedure
Primary problem: Procedure

Narrative: BACKGROUND: The VOR/DME RW 31 approach at PAO brings aircraft into PAO on an approximate 290 heading directly over the runway 32 departure end at Moffett Filed (NUQ). During the event; PAO was under IMC weather conditions with rather good visibility and a low overcast ceiling of 700 feet.EVENT: While working Local Control (LC) at PAO; a Aircraft X checked in on the VOR approach. I acknowledged Aircraft X and asked them to report the bases of the clouds when they break out. Several minutes later; the MSAW (Minimum Safe Altitude Warning) alarm sounded and I immediately looked at the radar display to see if I needed to inform Aircraft X of an unsafe altitude. It was not Aircraft X; however; that caused the alarm. Instead; Aircraft Y had just popped up climbing off NUQ runway 32 directly under and behind Aircraft X on approach. At the same time the MSAW; NUQ called via the shout-line to advise me of the conflict and I inquired as to whether or not the TRACON had released them with my Aircraft X crossing their departure corridor. NUQ said 'Affirmative; Aircraft Y on a 360 heading.' I looked out the window to see if I could make visual contact with the aircraft; but was only able to see Aircraft Y briefly before they disappeared into the ceiling. I then attempted to coordinate with NCT (Toga sector) to understand if there was anything I needed to do to help keep the aircraft separated or try and reestablish separation (as it appeared there was not any standard separation). NCT asked me to call them back two minutes later and then I replied that they could call me back when they had time; as now I was just curious as to where the miscommunication has occurred. NCT did not return my call and I did not call them back or press the issue further because it sounded like training was in progress and I wanted to avoid introducing more distraction.I did not quote traffic to Aircraft X because they were still in the clouds and Aircraft Y was behind them the entire time. My attempts to visually identify the aircraft were futile because of the clouds. As the event occurred; it seemed that coordination was needed more than a traffic alert; that's why I attempted to call NCT and corresponded with NUQ when they called. Since NCT did not return my shout-line coordination/call; I do not know if this event was even categorized as a loss of IFR separation. There may have been a rule or procedure applied (maybe something to do with divergence) that allowed this Aircraft Y to depart directly underneath Aircraft X; but based on the proximity of the two aircraft and the hurried tone of the NCT and NUQ controllers; I believe there was a major error in coordination and somehow Aircraft Y was released several minutes early/rolled several minutes late.If this was a legal maneuver; I would recommend that in the future; NUQ or NCT provide PAO with a 'rolling call' to let the LC know that a large aircraft will be tagging up directly beneath the VOR approach aircraft. This type of call would have lessened my reaction and had me prepared and possibly even advising Aircraft X that an aircraft is departing NUQ and they may see them either out the window or on their traffic display. If this was not a legal maneuver; however; and coordination was majorly mishandled; then I would recommend a review of the procedures for releasing aircraft off of NUQ while PAO has VOR approaches in use. I don't intend to speculate on all of the outcomes this scenario could have ended with as I do not know all the details from each party involved; but had the NUQ departure been an aircraft with greater vertical climb performance than Aircraft Y [military transport]; the two aircraft would have come into such close proximity with one another that the outcome begins to become unthinkable. The elements that kept these two aircraft separated were 1) the slow climb performance of Aircraft Y and 2) the fact Aircraft X had not descended as low as they were currently authorized to following the approach.The FALCON showed the two aircraft at their proximity on the first radar sweep after Aircraft Y tagged up. Several radar sweeps later; Aircraft Y and Aircraft X were at a proximity of 0.93 NM and 0 feet.




Synopsis: PAO Tower Controller reported a loss of separation between an IFR GA aircraft inbound to PAO and a departure off Moffett Field (NUQ).