Spokesman Alfredo Scoccimarro said the cancer was on the right side of the thyroid gland, but had not spread to other parts of her body.
It had been discovered during a routine medical examination on December 22.
More from GlobalPost: Cristina Fernandez de Kirchner wins re-election in Argentina
Fernandez, 58, who recently began her second term as president after a landslide election victory, will have an operation on January 4.
According to the BBC, the cancer has not metastasized or affected Kirchner's lymph node. The prognosis, according to the doctor, is very good. This type of cancer has a high survival rate if treated early, specialists said.
Fernandez will step aside for 20 days while she recovered from her surgery, with Vice-President Amado Boudou acting as president until January 24, the BBC reported.
Fernandez's election victory came a year after her husband, former president Nestor Kirchner, suddenly died of a heart attack.
More from GlobalPost: How Cristina turned her fortunes around
During her first term, marked by strong economic growth, Fernandez implemented social policies to benefit the poor, and remains popular, the BBC reported.
Her cancer diagnosis comes after that of Venezuelan President Hugo Chavez, Paraguayan leader Fernando Lugo, and former Brazilian President Luiz Inacio Lula da Silva.