Commercial Fixed Wing
Air Traffic Control Fully Certified
Air Traffic Control Time Certified In Pos 1 (yrs) 4
Confusion; Communication Breakdown
ATC Issue All Types; Conflict Ground Conflict; Less Severe; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance; Ground Event / Encounter Other / Unknown; Ground Incursion Runway
Airport; Procedure
I crossed Aircraft Y from RWY 22R at taxiway golf; and put Aircraft X in line up and wait. I observed Aircraft Y cross and come to a stop on taxiway B at which point he looked clear of the runway from my point of view and on the ASDEX. I still waited until I saw Aircraft Y moving ahead slightly; and overheard Ground Control issue instructions to taxi via Alpha. Then issued Aircraft X a takeoff clearance. Aircraft X took off and then advised me airborne that an aircraft wasn't clear of the runway.  The aircraft was clear of the runway from my point of view; and I issued a takeoff clearance after seeing him taxi up a little. I should have verified with Ground that he would not be held there for a prolonged period of time.
We were cleared onto hold Runway 22L at taxiway W. Aircraft Y was crossing 22L around mid-field. First Officer's takeoff. We were cleared to takeoff when Aircraft Y appeared to have crossed the runway. During takeoff roll (high speed regime prior to Vr) it became apparent that Aircraft Y had stopped after crossing the runway but with its tail not clear of the runway environment but not overhanging the runway itself. I advised the First Officer of the incursion and takeoff was continued. Passing behind Aircraft Y our aircraft attempted to veer to the right. We assume that Aircraft Y had increased its thrust to begin taxiing and our aircraft attempted to weathervane to the right as a result. The First Officer maintained proper track and rest of takeoff was uneventful. We advised EWR Tower after takeoff that Aircraft Y had not been clear of the runway. Had we been a light aircraft; or had there been other complicating issue there may have been more of an issue with aircraft control passing through Aircraft Y's engine thrust.
EWR Controller and an air carrier flight crew reported another air carrier's tail was not clear of the runway environment; resulting in a runway incursion and jet blast event.