"It is totally false, they remain together and they are very well," Shakira's chief publicist in Colombia, Rodrigo Beltran, told Efe.
He said the singer decided to clear the air after the breakup rumors circulated in European and Latin American media and on social networks.
"Good luck to the Spanish team this week and to my No. 3, muah! @3gerardpique . Shak," the singer tweeted.
Shakira, 34, and the 24-year-old Pique, who plays professionally for FC Barcelona, went public with their romance last year.
The multiple-Grammy-winning music icon will be honored at next month's Latin Grammy awards gala for her extensive philanthropic activities.