The ministry said that the Mu variant was found in a woman in her 40s who arrived on June 26 from the United Arab Emirates.
The other case was with a woman in her 50s who arrived from the United Kingdom on July 5.
The Mu variant, also known as lineage B.1.621, was first detected in Colombia in January 2021. There have been outbreaks in South America and Europe.
The WHO said the variant has mutations that indicate a risk of resistance to vaccines and stressed that further studies were needed to better understand it.