The Manchester United striker, 25, missed Belgium’s 3-1 win over Russia on Thursday because of the issue.
He last featured in United’s 2-0 defeat against Arsenal at the Emirates Stadium, missing the FA Cup quarter-final defeat against Wolves.
While head coach Roberto Martinez initially hoped Lukaku would be able to face Cyprus on Sunday, Belgium confirmed the striker would miss the trip.
“@RomeluLukaku9 will not travel with us to Cyprus this morning due to a foot injury,” they wrote on Twitter on Saturday.
— Belgian Red Devils (@BelRedDevils) March 23, 2019