B777-200 CREW WAS CLRED INTO POS AHEAD OF A LNDG ACR ACFT AT RJAA.

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ON AUG/FRI/03; I WAS ACTING AS THE FO OF FLT FROM NRT TO ZZZ. 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. WHILE TAXIING; GND CTL ASKED IF WE WOULD BE READY AT THE END IMPLYING THAT A TKOF CLRNC WAS IMMINENT; TO WHICH I REPLIED 'AFFIRMATIVE.' AT THAT TIME WE WERE INSTRUCTED TO CONTACT TWR. UPON CONTACT WITH THE TWR; 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 I READ BACK; 'ACR X POS AND HOLD RWY 34L.' AT THIS POINT THERE WAS NO RESPONSE FROM THE TWR INDICATING A CORRECT READBACK. UPON TAKING POS ON RWY 34L; ACR Y FLT CONTACTED THE TWR THAT THEY WERE INSIDE THE FINAL APCH FIX. TWR RESPONDED 'CONTINUE' WHICH IS A TYPICAL RESPONSE WHEN ANOTHER ACFT IS STILL ON THE RWY. NOTICING THE PROX OF ACR Y ON THE TCASII (APPROX 300-400 FT AGL) I KEYED THE MIKE AND STATED THAT ACR X WAS STILL ON THE RWY. SIMULTANEOUSLY; THE TWR INSTRUCTED; ACR 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. I REFUTED HIS STATEMENT THAT HE CLRED US INTO POS. SUBSEQUENTLY; WE WERE CLRED FOR TKOF. 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 I RESPONDED THAT WE IN FACT DID NOT HAVE A RWY INCURSION AND WE WERE CLRED ONTO RWY 34L. I REITERATED THAT WE WERE CLRED INTO POS; I READ BACK THAT WE WERE CLRED INTO POS; THAT THE 3 OF US ON THE FLT DECK HEARD THAT WE WERE CLRED INTO POS; AND THAT THE CTLR NEVER RESPONDED TO THE CONTRARY. THE SUPVR STATED THAT HE WOULD PULL THE TAPES TO REVIEW THE DIALOG. AT THE TIME OF THIS EVENT; THE WX WAS RPTED TO BE OVCST AT APPROX 200 FT; AND VISIBILITY WAS APPROX 1 MI. ADDITIONALLY; THERE WAS VERY LITTLE GND TFC AND NEITHER THE GND NOR TWR FREQS WERE CONGESTED.