Granma said Jagger, 72, was on a private visit "but it could be related to a concert that the Rolling Stones wants to give in Cuba."
Jagger, who was traveling with one of his children, was seen at a timba concert over the weekend given by the group Bamboleo in western Havana.
Granma said he also toured Old Havana and Cuban night clubs.
The Cuban newspaper quoted recent remarks by guitarist Keith Richards that the Stones could give a concert next month at Havana's Latin American Stadium, the island's biggest baseball stadium.
Stones bassist Darryl Jones and Bernard Fowler, a Stones back up singer, performed in Havana in February with the group The Dead Daisies.
Rock was frowned on in Cuba for many years for ideological reasons, but it has gained popularity over the past decade as the island has opened up.