ATC SPONSORED RWY INCURSION CREATES POTENTIAL FOR A COLLISION BTWN 2 ACR ACFT DURING A PLANNED OPPOSITE DIRECTION TKOF ON AN OCCUPIED RWY AT SAN; CA; THAT IS CAUGHT AND NEGATED BY ONE OF THE FLT CREWS.

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SAN WAS LNDG RWY 9 AND DEPARTING RWYS 9 AND 27. WE WERE READY FOR DEP HOLDING SHORT RWY 9. WE WERE #1 OF 2 ACFT WAITING FOR DEP. THERE WERE SEVERAL ACFT WAITING FOR DEP ON RWY 27. TWR HAD CLRED AN ACFT FOR TKOF ON RWY 27. ONCE THAT JET WAS AIRBORNE; TWR CLRED US; 'COMPANY FLT X; RWY 9; TAXI INTO POS AND HOLD; EXPECT NO DELAY.' WE ACKNOWLEDGED THE CLRNC; RAN OUR BELOW THE LINE ITEMS AND STARTED ACROSS THE HOLD LINE ONTO THE RWY. WHEN WE WERE CLRLY PASSED THE HOLD LINE AND ABOUT TO MAKE A TURN TO LINE UP ON THE RWY; WE HEARD FROM TWR; 'COMPANY FLT Y; RWY 27 CLR FOR TKOF.' WE IMMEDIATELY STOPPED THE ACFT AND BEFORE WE COULD SAY ANYTHING TO TWR; ACFT Y JUMPED ON THE RADIO AND SAID TO TWR THAT HE HAD AN ACFT HOLDING IN POS ON RWY 9. AS I REMEMBER; TWR DID NOT CANCEL COMPANY FLT Y'S TKOF CLRNC AND COMPANY FLT Y FURTHER STATED THAT HE WAS HOLDING SHORT OF RWY 27. WE WERE ABLE TO PERFORM 180 DEG TURN TO EXIT THE RWY AND REPOS OURSELVES AS #1 FOR DEP RWY 9. TWR CONFIRMED THAT WE WERE CLR OF THE RWY; THEN RECLRED COMPANY FLT Y FOR TKOF. AFTER ANOTHER ACFT DEPARTED RWY 27; WE WERE GIVEN A CLRED FOR TKOF RWY 9. ON THE HDOF; THE TWR CTLR APOLOGIZED FOR BEING THE SOURCE OF THE CONFUSION. I TOLD HIM THAT EVERYTHING WORKED OUT; NO HARM; NO FOUL; AND WISHED HIM GOOD DAY. THIS CHAIN OF EVENTS STARTED WITH POOR WX CONDITIONS THAT FORCED THE USE OF RWY 9 AND IT SLOWER LNDG MINIMUMS. THE CHAIN WAS BROKEN BY AT LEAST 3 ALERT CREWS THAT WERE CLOSELY FOLLOWING THE OP ON THE RADIO. THIS UNUSUAL RWY CONFIGN IS RARELY SEEN AND WHEN WE DO; IT'S BECAUSE OF ADVERSE WX CONDITIONS. I CAN ONLY IMAGINE THE WORKLOAD FOR THE TWR CTLR WHEN COUPLED WITH DARKNESS; POOR VISIBILITY; RAIN; GND CTL COORD BTWN 2 RWYS; DEP CTL COORD FOR 2 DIFFERENT DEPS; AND ANY OTHER PROBABLE DISTRS. WHEN THE WX GOES DOWN; THIS POTENTIAL PROB COULD FURTHER BE PREVENTED WITH FORCING ALL DEPS TO RWY 9; EXCEPT THOSE WITH DEFINITE PERFORMANCE CONSIDERATIONS. WHEN AN OPPOSITE DIRECTION DEP IS NECESSARY; ANOTHER SET OF EYES AND EARS IN THE TWR WOULD HELP AS A BACK-UP TO MAKE SURE THE RWY STAYS CLR. SUPPLEMENTAL INFO FROM ACN 603811: WE WERE INSTRUCTED TO TAXI TO THE RWY 27 HOLD AREA AND EXPECT A LENGTHY DELAY DUE TO INBOUND ARRS. ASKED TWR TO GIVE US 5 MINS NOTICE; AS WE WERE GOING TO SHUT DOWN ENGS. RAN APPROPRIATE CHKLIST AND WAITED. AFTER SOME TIME; TWR INSTRUCTED US TO START ENGS AND WHEN WE WERE READY; TAXI UP TO AND HOLD SHORT OF RWY 27. HE ADVISED US HE HAD 2 MORE TO LAND AND HE WOULD GET US OUT AFTER THAT. AS THE SECOND OF THE 2 ACFT WERE ROLLING OUT; HE CLRED ANOTHER COMPANY FLT X INTO POS AND HOLD RWY 9. THE FO AND I LOOKED AT EACH OTHER AND FIGURED THE CTLR HAD CHANGED HIS MIND ON THE SEQUENCE. COMPANY RESPONDED TO THE CLRNC AND I WATCHED HIM TAXI INTO POS AT THE OTHER END OF THE RWY. A FEW SECONDS LATER; THE CTLR CLRED US FOR AN IMMEDIATE TKOF RWY 27. WE CONTINUED TO HOLD SHORT AND ADVISED TWR THAT HE HAD JUST CLRED US FOR TKOF ON RWY 27 WITH COMPANY ACFT HOLDING IN POS AT THE OTHER END. THE CTLR SEEMED CONFUSED AND ASKED THE OTHER COMPANY FLT IF HE WAS ON THE RWY. HE RESPONDED YES THAT HE HAD BEEN CLRED INTO POS ON RWY 9. THE CTLR CLRED THE ACFT AND WE DEPARTED.