The heartfelt message was made during a virtual Iftar, which is the communal breaking of the fast, where he spoke out about the impact of the Covid-19 pandemic on the country.
"I can only say how deeply saddened I am by this tragic situation and how my heart goes out to all those who have lost their loved ones," he continued.
He also wished Muslims an Eid Mubarak ahead of the end of Ramadan. The end of Ramadan, during which Muslims fast during daylight hours for a month, is marked with a celebration called Eid.
The online event followed the State Opening of Parliament in Westminster, where Charles attended with his mother the Queen and his wife Duchess Camilla.
It was Her Majesty's first major public engagement since the death of Philip on April 9.
Charles has previously sat on the consort's throne when accompanying the Queen, but during this ceremony, he sat with Camilla on chairs of state - placed to the side.
Charles also recently sent out thank you cards following the passing and funeral of the Duke of Edinburgh to loyal fans who have offered their condolences.
The Prince shared a retro black and white photo of himself as a child, approximately nine or 10-years-old with his father, Philip, boating during a visit to the Isle of Wight in 1958.
The card read: "His Royal Highness has been enormously touched by the many generous messages that have been received in recent days; they have provided great comfort at this very sad time."