The 28-year-old Waimate native, who won silver in woman's trap shooting, caught a taxi on her own from the New Zealand club based at Rio's Sheraton Hotel back to the village, according to One News.
A source told One News Rooney became frightened and upset when the driver demanded 275 reais, 175 reais more than the pair agreed on at the start of the journey.
It is understood the taxi driver stopped the car and eventually accepted 100 reais, leaving Rooney out in the dark where a security guard came to her aid and arranged a private car to take her back to the village.
Security was in the spotlight in the lead-up to the games and has come under further question since the games began six days ago.
Several incidents in Rio have caused alarm, including a stray bullet piercing the media tent at the equestrian centre and a bus carrying journalists being struck by projectiles, and reports of athletes, diplomats and sports officials being robbed.
