Phungwayo, whose existing deal expires at the end of June, looks to be staying put despite attracting interest from Europe as well as PSL giants Kaizer Chiefs and Mamelodi Sundowns.
Musonda, though, could be loaned out having yet to score a goal for the Sea Robbers, according to a club official.
The 24-year-old Zambian penned a three-year contract with Pirates at the start of the year following spells with Africa Sport Youth Academy and Zenaco in his homeland.