B777 FLT CREW HAS RWY INCURSION AT RJAA.

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ON AUG/FRI/03; I WAS THE AUGMENTING FO OF FLT FROM NRT TO SEA. AFTER COMPLETING THE PRE-DEP CHKS; WE PUSHED BACK FROM OUR PARKING SPOT; STARTED ENGS AND PROCEEDED TO TAXI FOR TKOF FROM RWY 34L AT NRT. THE WX CONDITIONS WERE LIGHT NORTHERLY WINDS; WITH LOW (APPROX 200 FT AGL) CEILINGS AND 1 TO 1/2 MI VISIBILITY. WHILE TAXING; AROUND HALF WAY TO THE RWY; GND CTL ASKED IF WE WOULD BE READY AT THE END; IMPLYING THAT A TKOF CLRNC WAS IMMINENT; TO WHICH THE FLYING FO REPLIED 'AFFIRMATIVE.' AT THAT TIME WE WERE INSTRUCTED TO CONTACT TWR. UPON CONTACT WITH THE TWR; NEARING THE RWY 34L RUN-UP AREA; WE WERE INSTRUCTED TO 'CONTINUE.' AS WE APCHED THE DEP END OF RWY 34L; THE TWR INSTRUCTED US TO 'POS AND HOLD RWY 34L' TO WHICH THE FLYING FO READ BACK 'ACFT X POS AND HOLD RWY 34L?' AND COMPLETED HIS FINAL BEFORE TKOF CHKS. THERE WAS NOT HOWEVER; A RESPONSE FROM THE TWR INDICATING A CORRECT (OR INCORRECT) READBACK. UPON TAKING POS ON RWY 34L; ACFT Y CONTACTED THE TWR THAT THEY WERE INSIDE THE FINAL APCH FIX. ALL 3 MEMBERS OF THE COCKPIT OBSERVED ACT Y AS A TCASII TARGET (I BELIEVE THE INITIAL PICTURE SHOWED ACT Y NEAR THE FAF) TWR RESPONDED 'CONTINUE' WHICH IS A TYPICAL RESPONSE WHEN ANOTHER ACFT IS STILL ON THE RWY. NOTICING THE PROX OF ACFT Y ON THE TCASII (APPROX 300-400 FT AGL) THE FLYING FO KEYED THE MIKE AND STATED THAT ACFT X WAS STILL ON THE RWY. SIMULTANEOUSLY; THE TWR INSTRUCTED ACFT Y TO GO AROUND. TWR THEN QUESTIONED US AS TO WHY WE WERE ON THE RWY AND STATED THAT HE TOLD US TO HOLD SHORT. THE FLYING FO REFUTED HIS STATEMENT THAT HE CLRED US INTO POS (A POS THAT WAS CONFIRMED BY BOTH THE CAPT AND MYSELF). SUBSEQUENTLY; WE WERE CLRED FOR TKOF. IT IS OF NOTE THAT WE COULD MAKE OUT; ALBEIT BARELY; THE TWR COMPLEX FROM OUR POS. AFTER CONTACTING DEP; WE WERE NOTIFIED TO CONTACT 'APCH' ON ANOTHER FREQ; WHICH HAD A SUPVR ON THE OTHER END. IN HIS INQUIRY; THE SUPVR ASKED US WHY WE HAD A RWY INCURSION TO WHICH WE RESPONDED THAT WE IN FACT DID NOT HAVE A RWY INCURSION AND WE WERE CLRED ONTO RWY 34L. THE FLYING FO; IN CONCURRENCE WITH THE REST OF THE COCKPIT CREW; REITERATED THAT WE HAD BEEN CLRED INTO POS AND READ BACK AS SUCH; AND THE CTLR NEVER RESPONDED TO THE CONTRARY. THE SUPVR STATED THAT HE WOULD PULL THE TAPES TO REVIEW THE DIALOG. THE REMAINDER OF THE FLT WAS UNEVENTFUL.