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Semenya was not included in the team after consultation between her coach, Michael "Sponge" Seme and Athletics SA's interim leadership. Seme said Semenya was not yet ready for international competition.
"She is looking at the Commonwealth Games in India in October. We have agreed with ASA that Caster will not go to Kenya," said Seme.
"We are trying to organise a series of meets for Caster."
Seme and Semenya were scheduled to leave for Europe yesterday.
After spending 11 months in the wilderness, Semenya was allowed to run again as a woman by the International Associations of Athletics Federation (IAAF) on Tuesday.
This was after the IAAF had banned her from competing pending a gender verification investigation.
Semenya, a sports marketing student at the University of Pretoria, has not raced since winning gold at the World Championships in Germany last August.
She is expected to make her first return to the sport by competing at a track meeting in Finland on Thursday.
"Semenya will work towards reaching peak condition in order to be a part of the action at the Commonwealth Games in New Delhi, India in October," ASA said in a statement.
ASA leaders have also promised to get races for Semenya overseas so she is in great shape for the Commonwealth Games.