Ronaldo, Portugal's most-capped player and all-time top scorer, was benched for their first knockout game on Tuesday as they beat Switzerland 6-1, with his replacement Goncalo Ramos netting a hat-trick. Ronaldo made a late substitue appearance.
"The FPF clarifies that at no time did the captain of the national team, Cristiano Ronaldo, threaten to leave the national team at any stage in Qatar," it said.
"The level of commitment of Portugal's most capped international player was once again demonstrated ... in the victory against Switzerland."
Ronaldo has struggled to find the net since converting from the penalty spot in Portugal's group opener against Ghana, when he became the first player to score in five World Cups.
Portugal play Morocco in the quarter-finals on Saturday.
