"He (Bony) was away (at the African Cup of Nations) for a while and during that time Peter Crouch came into that side and did really well. It's been difficult for Wilf to get back in," Hughes told reporters on Friday.
"We've bought Berahino in the meantime, so that's an extra striker on the books. So he's just going to have to be patient, as all players have to be."
Berahino, who moved from West Bromwich Albion in January, has not scored a league goal in over a year and saw his career stall at his former club due to a series of off-field incidents.
Welshman Hughes, however, has been impressed with the hard yards Berahino has put in on the training ground.
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"He's (Berahino) doing extra work over and above the main group on sharpness and finishing. We've been really impressed with him, particularly in terms of his finishing," Hughes added.
"He's clearly very much in my thoughts. It's only going to be a matter of time before he scores goals for us."
(Reporting by Shravanth Vijayakumar in Bengaluru; Editing by Hugh Lawson)
