The Football Associations of Ireland and Wales and the Irish Football Association want to reduce the Carling Nations Cup fee due to the Scottish FA.
However the FAI, IFA and FAW hope to avoid involving Fifa in resolving the dispute.
In a joint statement, the three bodies said they had "been in negotiations with the Scottish FA seeking a downward adjustment of their fee".
They added that this was "to give a more equitable share of the profits".
The tournament took place in February and May and was won by the Republic of Ireland, Scotland finishing second.
Each nation played each other once in a group format with all fixtures taking place in Dublin.
The joint-statement from the FAI, IFA and FAW was released in response to media reports that the SFA was considering reporting the FAI to Fifa over the non-payment of £1.2m, the fee agreed for Scotland's participation.
The statement added: "The competition...returned a profit derived from television rights, sponsorship and ticket sales.
"It is disappointing that this matter has come into the public arena while the four associations are still trying to reach agreement.
"The FAI, IFA and FAW will not be making any further comment to give proper space for those discussions to take place."
The SFA told the Press Association that "private discussions are ongoing".