Hughes spent £17m to lure the Paraguayan down the M61 from Blackburn, but was already aware his City debut would be put on hold due to knee surgery.
With Emmanuel Adebayor having since been recruited from Arsenal, Hughes has no need to push the 27-year-old back into action too soon.
And the City chief intends to let Santa Cruz recover at his own pace in the hope his side will gain long-term benefits.
``We knew Roque would have a period of rehabilitation when we signed him, but we have good options up front,'' Hughes told www.mcfc.co.uk.
``If we can, we want to give him the time he really needs, rather than getting him back early and having him at 70%.
``Rather than bring him back too soon. I would rather give him the time that he needs. We are hoping by the end of the month he will be available.''
With just three days to go before his new-look side visit Blackburn, it promises to be a busy time for Hughes.
It is expected City will lodge another bid for Joleon Lescott, although Everton are giving no sign of being interested in doing a deal, even if the Eastlands outfit increase their most recent £18million offer.
Toffees boss David Moyes was unequivocal in his response to Lescott's official transfer request yesterday, and the Scot is showing no sign of softening his stance.
``I have said all along that I have no intention of selling my best players,'' he told www.evertonfc.com.
``Joleon is simply not for sale.''
It means Hughes will almost certainly have to utilise his present squad at Ewood Park, although, like Santa Cruz, neither Vincent Kompany nor Michael Johnson will be involved.
Kompany underwent a toe operation last month, while Johnson is still two weeks away from a return to action after suffering a minor setback in his recovery from an abdominal complaint that ruled him out for most of last season.