The Premier League have written to Portsmouth this week ordering the club to pay the money to Spurs.
Although Begovic never moved to Tottenham, the clubs had agreed a joint fee with Younes Kaboul with the agreement that £1million would be paid to Spurs if the Bosnia international moved elsewhere.
Begovic eventually moved to Stoke, shortly after which Pompey went into administration, since when they have been disputing whether they actually owe Tottenham the money.
Now the Premier League have become involved and have been satisfied that Portsmouth are contractually obliged to pay Spurs the £1million.
If the money still does not materialise, the league will top-slice it off the cash due to be received by Portsmouth at the end of next year in parachute payments and pass it on to Spurs directly.