Fernandez quit following the defeat in the Senate of a controversial export tax on certain crops, La Nacion reported. His resignation came after days of speculation that he would leave the administration.
Last week, an export tax bill covering some Argentine crops promoted by the president was defeated in the Senate. Kirchner then canceled the tax amid widespread protests.
Massa is a former head of the social security agency, Mercopress reported.
"I'm going to do my utmost and I humbly call on all sectors to contribute to help build a better and fairer country," Massa said following his appointment.
Kirchner, he said, "asked me to generate consensus, to work closely with governors, senators and deputies, and to continue with the government's effort to benefit the Argentine people".
Fernandez is the second Cabinet to resign from the Kirchner administration. The first was Agriculture Secretary Javier de Urquiza.