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With skipper Keving Muscat facing a suspension in two weeks time and with Mark Phillips and Paul Robinson ruled out through injury for the rest of the season, Rees is needed back at The Den.
The 21-year-old was just coming to the end of his second sucessful month with the Conference Side which saw The Shots being beaten just twice in the 10 games he played.
Millwall's assistant manager Ray Wilkins said: "Not only has the first team squad been decimated by injuries but we have also had difficulty fielding a reserve team.
"Under the circumstances we thought it was best that Matt returns to us and get a good physical test in our reserve team at Reading on Wednesday."
Rees will be unavailable for Millwall's cup tie against Walsall, however, having played in Aldershot's second round exit at the hands of Colchester United at the weekend.