The programme for the swimming sessions was approved by the International Olympics Committee (IOC) on Thursday but the exact timings for events at the Aquatics Centre were not released.
Media reports have suggested that the delay was due to American broadcaster NBC's desire for swimming finals to be held in the morning to enable peak viewership in the United States.
Although the complete swimming schedule has yet to be ratified by the IOC and Tokyo organisers, the JSF conceded defeat in its attempts to hold the finals -- one of the most popular Olympic events in Japan -- later in the day.
"The Japan Swimming Federation has made our effort to have finals to be held in the afternoon. It is highly regrettable that the 2020 Tokyo Olympics swimming finals were reportedly decided to be held in the morning," the JSF said in a statement.
"Even though finals will be held in morning time, we will continue to make efforts to achieve the result that can fulfil expectations of Japanese nationals."
At the 2008 Beijing Games, the last Summer Olympics held in Asia, the swimming finals were held in the morning and a repeat of that scheduling is fully expected in Tokyo.
In 2014, NBC signed a $7.65 billion deal with the IOC giving it exclusive Olympics broadcasting rights in the United States until 2023.
Swimming world governing body FINA could not be reached for comment, although media reports claim they have agreed to morning finals.
Tokyo 2020 organisers, meanwhile, refused to confirm any changes to the schedule and said discussions were ongoing with various stakeholders.
"We are aware of FINA's announcement," Tokyo 2020 spokesman Masa Takaya said in a statement.
"As decided during the recent IOC Executive Board meeting, we will continue discussions to come to an agreement among the IOC, FINA and Tokyo 2020."
Next Tuesday (July 24) marks the two-year countdown to the start of the Games.
(Reporting by Jack Tarrant; Editing by John O'Brien)
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