The Evening Chronicle says it is believed that he told United chiefs he wanted to stay and fight for his place, however, director of football Joe Kinnear, who said last month he would have "final say" on transfers, is thought to have sanctioned the departure.
But the popular utility player was told that the Magpies wanted to cash in because he was nearing the end of his current deal.
Having been notified he wasn't wanted, Perch had little choice but to join Wigan Athletic.
Perch said: "I understand Newcastle's new transfer policy. Time will tell if that is the right route. But I loved it there, the fans are incredible, I will never forget them."