The 2011 bronze medallist had been scheduled to compete in the 100, 200 and 4x100 relay in Moscow, but she pulled out of the Sunday's 100 heats.
The federation said the withdrawal was "related to doping matters," adding that it was notified Thursday by the IAAF of the case and said it was "premature and inappropriate" to comment further since the case was still being dealt with.
The 26-year-old Baptiste set a national record of 10.83 seconds this year and was third in the season standings, which made her a credible medal contender at the worlds.
In the same event, 2011 silver medallist Veronica Campbell-Brown of Jamaica was suspended from competition while a disciplinary panel reviews her doping case.
Along with Baptiste, the Trinidad and Tobago federation said that Semoy Hackett was also missing from the world championships related to doping issues.
"The absence of both athletes is related to doping matters of varying degrees and complexity," the statement said.
The 24-year-old Hackett served a six-month doping suspension in 2011. Because of that, Trinidad and Tobago was stripped of its fourth-place finish in the 4x100 at the 2011 world championships in Daegu, South Korea.