Phungwayo arrived at Stars as a free agent in September 2017 after his contract at Orlando Pirates was not renewed, and has now entered into the last four months of his deal with the Bethlehem side.
The 31-year-old left-back has played 17 matches in all competitions this season.
Mokoena says the club is currently focused on "important" things like saving the club's status.
"My man, I have got bigger issues right now, I'm not yet worried about that, that's what I will tell you," he tells KickOff.com.
"I have got bigger issues in front of me. I have bigger issues than the contract of Patrick Phungwayo. I'm sure you can see what's happening. The last thing that is on my mind is the contracts of the players."
The 2018 Nedbank Cup champions are currently 14th on the Absa Premiership table with only one point separating them from 15th-placed Chippa United.