Media reports said Onyango was no longer training at the club in a bid to try and force a move away to the African champions.
But a Maritzburg statement denies the claim.
“The story as presented misrepresents the brief discussion had with a journalist when he asked the chairman (Farouk Kadodia) why Brian Onyango was not with the team at Richard’s Bay,” said the club.
Maritzburg played last weekend at a tournament in Richard’s Bay against Lamontville Golden Arrows.
“As far as the club is concerned, Brian is in Kenya sorting out some paperwork and will be back before the end of the week,” added the statement.
Onyango, 23, has been at Maritzburg for the last two seasons after initially signing for Santos in Cape Town.