Mancini had hoped the 22-year-old would help City triumph in Europe.
But Johnson's progress seems to have stalled and he is some way from being ready for first-team action.
Fading star: Michael Johnson has struggled with injuries
The England Under 21 player - a product of City's youth system - was out for a year with abdominal problems and a knee-ligament injury.
There have been loan enquiries, most recently from Leeds and Leicester, but Mancini is keeping him for now, and Johnson appeared for the reserves last night. If there is no progress in the coming weeks, he is likely to be sold this summer.
This will disappoint many who had high hopes when he broke into the first team under Sven Goran Eriksson in 2007.
City are re-evaluating their academy, with the flow of talent drying up and Mancini struggling to find the four homegrown players he needs for his 25-man European squad next season.
Johnson, Shaun Wright-Phillips and Nedum Onuoha - who is on loan at Sunderland - are unlikely to be at City.
The future of Slovakia midfielder Vladimir Weiss - at Rangers this season - is unclear.
This leaves only defender Micah Richards as homegrown, so City could start next season with a European squad of only 21 or 22 players.
Mancini's men need to build on a goalless first leg in tonight's return Europa League last-32 match against Aris Salonika of Greece. Richards and James Milner were added to the injury list yesterday and midfielder Nigel de Jong is not yet fit.
'I hope (De Jong) can recover quickly because he's an important player,' said Mancini.
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