World Baseball Softball Confederation (WBSC) President Riccardo Fraccari has described the behaviour of Tokyo 2020 as "inexplicable".
Talks are currently ongoing regarding the schedule for men's baseball and women's softball at the Olympic Games in the Japanese capital.
The sports are each returning to the Olympic programme following a 12-year absence since they last appeared at Beijing 2008.
Fraccari has claimed that ensuring a round-robin format remains the WBSC's priority as this would ensure more games for participating players.
Tokyo 2020, however, maintain that a group format consisting of two pools of three teams would be best rather than a round-robin competition.
"We have to face the management of the 2020 Olympics in Tokyo, which is resulting to be very problematic and demanding, mostly due to an inexplicable behaviour of the Organising Committee," Fraccari said during a speech at the International Federation's Ordinary Congress at the Gaborone International Convention Centre in Botswana.
"We have to communicate and organise the Olympic qualifier, which not only will implicate a hard work for WBSC, but also a great commitment for all of you.
"We have to work together to show the international sports community that, as baseball and softball, we are a strong sport, a big movement which represents millions of athletes that work hard on a daily basis, even under difficult conditions and that their deepest desire is to be part of the Olympic family."
The Italian has implied that the round-robin format would make it more likely that Major League Baseball players would be permitted to participate because the league would be less likely to let them leave to potentially play in only one or two matches.
Tokyo 2020 sports director Koji Murofushi claimed that two pools would be best for their current plan to only use one primary stadium, in Yokohama for both men's baseball and women's softball.
Tokyo 2020 are currently finalising the detailed competition schedule for all sports in conjunction with the International Olympic Committee.
It is a process that in August they hoped would be finished in the next "six to nine months".
At present, one baseball and one softball game is expected to take place in Fukushima, more than 300 kilometres to the north of Tokyo.
The WBSC hope that this will be the first game of each competition in order to minimise travel and other logistical challenges.
Matches in Fukushima would be symbolic following the 2011 earthquake and tsunami in the region which left 16,000 dead.
The world governing body have also repeatedly called for a second venue in Tokyo but that request has been denied by Japanese organisers.
Fraccari has claimed they would be prepared to accept the one main stadium plan so long as they get their way over the round-robin format.