Quarantine officials at Ngurah Rai International Airport detained Andrei Zhestkov on Friday after he passed through a security screening before a planned flight back to Russia.
According to authorities, the two-year-old primate was found sleeping in a rattan basket. Mr Zhestkov prepared for the trip by packing baby formula and blankets for the orangutan.
“We believe the orangutan was fed allergy pills which caused him to sleep. We found the pills inside the suitcase,” Bali conservation agency official I Ketut Catur Marbawa said in a statement.
“[Zhestkov] seemed prepared, like he was transporting a baby,” he added.
Mr Zhestkov claimed that he was gifted the orangutan by his friend, who bought the primate for $3,000 (£2,271) from a street market in Java. The 27-year-old added that he was informed by his friend had him he could bring home the orangutan as a pet.
Officers also found two geckos and five lizards in the Russian's suitcase, Reuters reports.
Mr Zhestjov is now facing up to five years in prison and $7,000 in fines for smuggling.
Orangutans are a critically endangered species, according to the International Union for Conservation of Nature, with only about 100,000 remaining worldwide. Threatened by deforestation to make way for palm oil plantations, campaigners say a key step towards ensuring the species survives is reconnecting the fragmented forests the primates are spread across.
Illegal wildlife trade is rampant in Indonesia, despite efforts by authorities to crack down on smugglers.