The police force, which lost a High Court case in 2012, has already paid back £1.2m to the football club.
The figures emerged after the court examined the latest stage of the dispute, for charges over three seasons between 2009 and 2012.
The force said it would now work with the club to agree what money, "if anything", remains outstanding.
Two years ago, the High Court ruled the force overcharged for "special police services" between 2009 and 2012.
Leeds United had argued policing streets and car parks near its Elland Road ground was the force's responsibility and the club should not have to pay.
The High Court ruled in the club's favour and West Yorkshire Police lost a subsequent appeal against the decision.
The judge, Sir David Eady, said one area of dispute remaining related to how charges should be made for the 2012-13 and 2013-14 seasons.
Revealing details of developments in the case in a written analysis, following a further hearing in June, the judge said both parties had failed to agree a formula to calculate the appropriate rebate.
Sir David said the force had "repaid the rebate it thought due" and "claims now that no more is owed".
Assistant Chief Constable Mark Milsom said: "West Yorkshire Police has already repaid the club £1,238,816 following the original judgment.
"The ruling today makes clear that the force and the club should now work together to agree what, if anything, remains outstanding.
"We welcome the opportunity to now meet with the club."

Dickenson, 23, scored four goals in 78 appearances for the Gills across two seasons after joining from Brighton.
He was released by the League One side in May and joins on a two-year deal.
Ex-Millwall trainee Peter, 19, has signed a one-year deal after spending the season half of 2015-16 on trial with the U's Under-21 side.
He will be available for both the under-21 side and first-team as John McGreal makes his fifth and sixth signings since becoming U's boss.
Forward Denny Johnstone, midfielder Courtner Senior and defenders Luke Prosser and Ben Wyatt have all joined.
Find all the latest football transfers on our dedicated page.
Leeds United claims West Yorkshire Police still owes the club £800,000 for overcharging policing at home games.
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Colchester United have signed former Gillingham versatile left-back Brennan Dickenson and ex-Chelmsford City centre-back Dexter Peter.