Nippon Professional Baseball commissioner Ryozo Kato held a meeting with representatives of the 12 teams and issued an apology for his handling of the situation.
"I've caused a lot of trouble for the fans, players and people connected to the game," Kato said. "Baseball is very important in Japan's sporting culture and I have to carefully reflect on my responsibility to the game."
Japan's 12 teams agreed to have a third party investigate the issue of why NPB secretly made its baseballs livelier.
Kato, a former Japanese ambassador to the United States, indicated he would not resign and vowed to work toward reform within his organization.
NPB acknowledged this week for the first time that a new ball was introduced at the start of the season, resulting in a sharp increase in home runs.
Many players in Japanese baseball have criticized NPB for a lack of transparency.
There were 939 home runs in 2011 and 881 in 2012. This season's tally stood at 512 as of Tuesday, on pace for a season total of 1,297.
NPB previously denied this year's increase in home runs had anything to do with changes to the baseball.
NPB secretary general Kunio Shimoda said the issue was kept secret in order "to avoid confusion."