Rosa, held by police last week for questioning along with fellow Italian coach Claudio Berardelli, denied the charges and was remanded in custody. Berardelli has not been charged.
Kenya, renowned for its distance runners, has faced frequent allegations of doping, with some 40 cases reported in the past four years.
The International Olympic Committee (IOC) said last month that competitors from Russia and Kenya, given the recent history of doping in both countries, would have to be screened individually before being allowed to participate in the Rio Games next month.
Rosa, who runs Italy-based Rosa & Associati, was charged with "conspiracy to injure a person in his profession" contrary to Kenyan law, his charge sheet showed.
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One of the six counts under the two charges stated that Rosa, with others not in court, conspired to administer a prohibited substance to injure the profession of athlete Rita Jeptoo.
Jeptoo is a Boston and Chicago marathon winner who faces a doping case. The court said it would rule on a bail application by Rosa's defence on Monday.
The defence has also applied to the court to release Rosa's travel documents to enable him travel with his athletes to events in Europe and Latin America and the court will also rule on the application on Monday, Rosa's lawyer said.
Kenyan President Uhuru Kenyatta signed an anti-doping amendment bill into law last month after the World Anti-Doping Agency (WADA) said Kenyan legislation passed in April needed further changes to comply with WADA's code.
(Reporting by Humphrey Malalo; Writing by Duncan Miriri; editing by Ralph Boulton)
