Mr Santos, 61, says the cancer has been detected early and estimates his chances of recovery at 97%.
The announcement comes a week before the government enters landmark peace talks with Farc rebels to try to end nearly five decades of conflict.
Mr Santos, who took office in August 2010, is the latest Latin American leader to be diagnosed with cancer.
Others have included Luiz Inacio Lula da Silva of Brazil, his successor Dilma Rousseff, Venezuela's Hugo Chavez, Fernando Lugo in Paraguay and Fidel Castro in Cuba.
On Monday, Mr Santos said in a statement: "I have carried out all the routine exams recommended by the doctors, and there has been an abnormal growth of the prostate specific antigen."
He said he would carry on with his duties and was travelling to Peru for a summit with Latin American and Arab leaders later on Monday.
"With God's help, this will turn out to be only one of those challenges we all have to face in life," he added.
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