The News and the World and Sunday Mirror both carry front-page exclusives which, the BBC reported, could lead to the striker not travelling to Basel.
However the Press Association said an FA source expected all England’s players on the plane.
Manchester United star Rooney was instrumental in England’s 4-0 opening Group B victory over Bulgaria.
He had a hand in all three of strike partner Jermain Defoe‘s goals plus substitute Adam Johnson‘s strike, despite not finding the net himself.
He has not scored in his last 11 games for his country but ended a five-month goal drought – which took in the World Cup – in United’s 3-0 Premier League win against West Ham last week.
If Rooney does not start, either Carlton Cole and Darren Bent could come in as Peter Crouch and Bobby Zamora are both unavailable through injury.
Theo Walcott, who started on the right wing against Bulgaria, is another option for Fabio Capello up front.
Eurosport