The England captain suffered the damage during the first half of Newcastle United's 1-1 draw with Sheffield Wednesday at St James' Park on Saturday and he took no part after the interval.
Newcastle's manager, Ruud Gullit, cast doubt over Shearer's availability for England immediately after the match, saying: "If he couldn't play here, he won't be able to play for England."
United have denied that there is any rift between Shearer and Gullit after reports that the two disagreed over the injury.
Shearer was the only player not expected to meet up with the rest of Glenn Hoddle's squad, but there are doubts over Paul Scholes, who suffered a similar injury after scoring twice during Manchester United's 3-2 victory over Blackburn Rovers, and Leicester's Emile Heskey. He missed his side's 3-2 defeat at West Ham United after picking up an ankle problem during the Worthington Cup victory over Leeds United in midweek.
The Football Association's spokesman, Steve Double, said the injured players would be examined by England's medical staff before any withdrawals are announced.
"We are expecting everybody down with the exception of Alan Shearer, who's having a scan on his injured hamstring in Newcastle in the morning and will be in touch with Glenn after that,"Double said .
Hoddle is already without the injured Liverpool striker, Michael Owen, for the friendly against the Czech Republic, and Shearer's absence will force him into a re-think his attack. Dion Dublin, who continued his spectacular start at Aston Villa, with a hat-trick at Southampton on Saturday, is one alternative as is Owen's club-mate, Robbie Fowler, who scored a penalty in Liverpool's 3-1 home defeat by Leeds, is another. Ian Wright, still scoring after his move from Arsenal to West Ham, could also come into the reckoning.
Reports put Scholes's injury down to the Old Trafford pitch, which has cut up over the last two or three games and is being relaid ahead of United's next home match with Leeds in a fortnight's time.
Gareth Southgate is expected to join up with Hoddle's squad, but his arrival could be delayed because he wishes to attend the birth of his first child. The Aston Villa defender expects to arrive at Bisham Abbey this afternoon after his wife, Alison, has given birth.
Villa have a club record four players in the squad, with Southgate joined by Paul Merson, Dion Dublin and Lee Hendrie.
The FA chairman, Keith Wiseman, says there is "nothing wrong or unusual" about the FA providing financial help to the Football Association of Wales. Wiseman has pledged a pounds 3.2m grant to the hard-up FAW, spread over eight years is adamant that such assistance is "commonplace."
Wiseman admits his actions are "still being discussed inside the FA" but hopes the matter will be "resolved quickly".