Inter completed the loan signing of Lukas Podolski from Arsenal last week and the Serie A giants are now set to welcome Shaqiri to the San Siro on a similar deal after club officials flew to Munich to conclude talks with Bayern.
A statement by Inter Channel, the official television network of Inter, said: "Total agreement between Inter and Bayern for the transfer of Shaqiri. Only the signature is missing."
Media reports earlier said Shaqiri did not train with the rest of Bayern's squad on Thursday, a sign that he could be preparing to depart for Milan where he is expected in the coming days, according to the Gazzetta dello Sport.
It said Shaqiri, who has not played regularly at Bayern in the face of competition from Franck Ribery and Arjen Robben, would sign a six-month loan deal that has cost Inter €2 million but could join Inter permanently on a four-year deal worth another €14 million at the end of the season.
After a three-year absence from the Champions League, 2010 champions Inter are desperate to qualify for next season's competition.
Roberto Mancini's side currently lie 11th in Serie A, 18 points behind leaders and champions Juventus and eight behind Lazio in the third and last Champions League qualifying spot.