The two allegedly pulled off the theft of the drugs during the recent extended weekend holidays to mark the Christmas celebrations.
Hospital employees who returned from the holidays noticed the drugs had gone missing and quickly contacted police.
Investigations led to the arrest of the pharmacist and his accomplice, both in their 30s.
The police believe the two were planning to sell the drugs to an illicit drug syndicate.City deputy CID chief Asst Comm Khairy Ahrasa confirmed the arrests but declined to comment further.
Minister Datuk Seri Liow Tiong Lai said a police investigation was ongoing and an internal probe was also being conducted