Mackail-Smith went down suddenly at Ashton Gate on Tuesday after breaking away from Liam Fontaine's challenge just before the break, and immediately signalled for medical attention.
The Seagulls boss admitted his fears over the striker's injury and his concerns over the lack of strikers in his squad.
Poyet said: "It looks bad. Craig could be out for two or three months so his season may be over.
"I don't like the emergency loan system, but I am not so stupid that I won't use it as we are now very short of strikers.
"I'll start looking for a new striker tomorrow. It was meant to be my day off, but now I expect to spend most of it on the phone."