Spurs boss Mauricio Pochettino said the 20-year-old would be out for "a few weeks" after leaving him out of his squad to play Arsenal on Sunday.
Pochettino said Alli "twisted his knee in a clash with a team-mate".
England play Scotland on Friday and Spain the following Tuesday at Wembley.
"I hope it is not a big issue, it's bad luck, he's an important player for us," Pochettino added.
"He will be out for a few weeks. We need to assess him today, tomorrow. That is football and sometimes it happens."
Tottenham midfielder Dele Alli has been ruled out of England's World Cup qualifier with Scotland and friendly against Spain after suffering a knee injury in training.