Johnstone has been sent home from the England camp, who are preparing to face Belgium in an international friendly on Tuesday, after picking up an elbow injury at the weekend.
With Palace likely to remain in the Premier League next season after improved results under Oliver Glasner, Johnstone would have been looking to maintain his place as a backup with the Three Lions.
The 31-year-old won back his place in the Eagles' side under Glasner after dropping to bench in the final few games of Roy Hodgson's reign at the club.
In the four games after Johnstone regained his place, Palace took five points, and also kept a clean sheet against Burnley at Selhurst Park.
However, the Evening Standard claim Johnstone could miss the rest of the season, jeopardising his chances of being part of Gareth Southgate's squad in Germany.
Jordan Pickford is the undisputed number one, but Johnstone has become the third-choice goalkeeper of late thanks to his performances with Palace.
Aaron Ramsdale remains second-choice, but there is now a possible battle for the final slot in Southgate's squad.
James Trafford has been called up to the current squad despite being dropped by Burnley last week, while Jack Butland is also having a fine season with title-chasing Rangers in Scotland.
At Selhurst Park, Johnstone is set to be replaced by Dean Henderson, who himself may have ambitions of working his way back into the squad after his injury nightmares of the last two years.
Should Johnstone not feature much until the end of the season, Southgate may be wary of a lack of match sharpness, should the unlikely scenario occur that the third-choice stopper would be required.
Palace remain eight points above the relegation zone, and spirits are higher despite throwing away two points late on against Luton Town in their last outing.
Glasner takes his Palace side to the City Ground to face Nottingham Forest on Saturday on their return to action, with their hosts set to be galvanised after receiving a four-point deduction during the break.
A win for the Eagles would extend the gap to 11 points on the bottom three with eight gameweeks left of the season, going a long way to ensure their safety, but Johnstone will join the likes of Marc Guehi and Michael Olise on the sidelines for that one.