Government spokesman Nicos Christodoulides said the president underwent a routine check-up on Tuesday when it was discovered he needed surgery.
The operation to repair a narrowing of the mitral valve, an open heart procedure, will be carried out "shortly", he said in a brief statement.
Damage to the mitral valve, the "inflow valve" for the left side of the heart, is not considered a life-threatening condition and repair is normally carried out using a catheter with a balloon on the end.
The conservative leader was elected president in February 2013, just days before Cyprus had to negotiate a painful USD 12.5 billion bailout with international lenders.
He is credited with steering the country from near-bankruptcy and ensuring the economy did not suffer a double-digit recession.
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