The 27-year-old was controversially omitted from the three-women marathon team for the Aug. 22-30 championships in Beijing, however, with Risa Shigetomo getting a spot in her place.
"When the only explanation we get is that strong runners have been chosen, you can't understand," Takahashi told the Kyodo news agency.
"With the focus on the selection for next year's Olympics, we need an announcement that will satisfy those who are left out. Transparency is essential."
Takahashi, a director of the Japan Association of Athletics Federations, knows well the pain of being left out of a team after missing out on defending her Olympic title in 2004.
"Personally, I think Tanaka was a step ahead," Takahashi added. "Shigetomo must feel very awkward as well. Regardless of whether an athlete wins or loses, we must do what we can to help them stay positive."
Shigetomo, who finished third in the Osaka Marathon in 2:26:39, is coached by Yutaka Taketomi, who also helps run the Japanese women's marathon team.
(Reporting by Nick Mulvennety in Sydney, editing by Peter Rutherford)
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