Tokyo 2020 President Yoshirō Mori admits that they will be unable to finalise their Olympic and Paralympic budgets until the division of roles between different Governments involved in the Games has been identified.
It comes as the International Olympic Committee (IOC) continues to pressure Japanese organisers both to finalise their budget and to keep it below the $20 billion (£16 billion/€18.8 billion) cap announced earlier this week.
Mori has so far refused to promise that they will make a reduction and maintains that they must work-out who is responsible for what before this can be done.
Construction costs for venues within Tokyo are the responsibility of either the Tokyo Metropolitan or Japanese National Governments, while the burden for those outside the capital city will be shared between these two bodies as well as the local municipal authority.
Transport and security costs are expected to fall under the remit of the National Government, although this also has not yet been fully finalised.
"The largest challenge for us is how the division of roles between the Organising Committee, the National Government, the Tokyo Metropolitan Government (TMG) and various other municipalities [outside Tokyo also hosting sports] has not been made clear," Mori, a former Prime Minister of Japan, said here today.
"As of today, we have not been able to identify division of roles involving the relevant parties.
"We have to decide on that in order to solidify the overall budget number."
A similar division of responsibilities between Municipal, State and Federal authorities was also a challenge in Brazil before the Rio 2016 Olympic Games.
It is still hoped that the first draft of Tokyo's overall budget will be finalised before the end of 2016 - although it may not be publicly disclosed until later.
A TMG Task Force warned in September that drastic changes must be taken to avoid the budget ballooning to ¥3 trillion (£22 billion/$30 billion/€26 billion).
This figure was more than four times the initial one given during the bidding phase and sparked widespread concern.
The Organising Committee's portion of the budget is expected to come to ¥500 billion (£3.55 billion/$4.7 billion/€4.2 billion), but a further breakdown between municipal and central authorities is not yet confirmed.
IOC vice-president and Tokyo 2020 Coordination Commission chairman John Coates, who spoke alongside Mori today, went into more detail about why exactly they thought Mori's latest cap was too high when it was still lower than other overall Games budgets.
He highlighted that it was the high cost estimations for overlay work at existing or temporary venues which is especially concerning.
The IOC believe that costs for certain elements, like renting space, could be far lower.
"We think they can make significant savings in security and other areas if the procurement starts earlier," the Australian added.
"The longer you leave it, the more expensive they are going to be because of the expense of labour and materials."
Coates did however strongly praise other elements of preparations following the two-day Coordination Commission visit.
This included engagement and promotional, hotel room numbers which "significantly exceeds" those in Rio [for the 2016 Games] and even in London [for 2012] and a sponsorship drive which has already seen 42 partners signed on.
He also praised Tokyo for appointing sports managers for 18 of the 33 sports on the programme before urging the final 15 officials to be sought.
This came after a second day of report on topics consisting of "sport, venues, venue management, test event management, energy, technology, National Olympic Committee services, the Olympic Village, accommodation and the Paralympics."
Two Coordination Commission visits are now going to take place every year starting in 2017.