The 26-year-old has not been involved in the first-team this season. He missed the opening two games, with Pools stating he was injured in training last week.
Pools last Friday signed Sunderland youth goalkeeper Joel Dixon on an emergency loan deal and he was on the bench at Stevenage, with Jonathan Barber, the club's youth team keeper on the bench at Port Vale in midweek.
Colin Cooper was asked about Rafferty's injury at this morning's pre-match press conference, but said it was something the club "was keeping in-house".
A statement about his future was released a little over an hour later.
Rafferty made three appearances at the end of last season, and made four first-team stats in total.
Pools are at home to Bury on Saturday, seeking to bounce back from successive defeats.
Cooper said: “It’s not the start we expected, certainly not on Tuesday. We all came in on Wednesday and watched Port Vale again from start to finish, which I felt was important.
“We saw things we did well, which we did, and things we weren’t great at – which were evident. We left the ground having watched it, it’s out of the system and now we prepare for the first home game, a fixture we are eager to get on with.''