The council threatened legal action against Customs and Excise after the £1,156,806 VAT repayment cheque went missing in October 1992.
The cheque, which was sent by normal post, was later cashed by an unknown person in Vienna.
But the council will not receive the full amount originally lost. In an out of court settlement Customs and Excise has only offered to reissue a cheque for £1m.
'We are out of pocket by £150,000 but that is better than being out of pocket by over £1m', said council leader Toby Harris.
He said he was pleased that Customs and Excise had conceded the point that the fault did not lie with the council.
At the time the cheque went missing the council criticised Customs and Excise for sending the repayment by post instead of transferring it electronically. 'If Customs and Excise are stupid enough to put such a huge cheque in the post, they must realise that if it goes astray, they will be pursued for repayment', said Mr Harris last year.
After the cheque went missing the council's finance department promised that all post would in future be opened in the presence of two finance staff.
Police are investigating the missing cheque and expect to fly out to Vienna in the near future to pursue their inquiries. They confirmed the cheque was intercepted before reaching the council and altered before being cashed.
Customs and Excise said it hoped to recover the lost money once the police investigation was completed. A spokesman said it was normal practice to send refund cheques in the post but this was under review.
Haringey's new cheque was delivered by hand.