The 32-year-old's contract was not renewed at the end of last season and the former Liverpool striker joined Stoke City on a free transfer in September.
"Michael is a fantastic player," Ferguson is quoted as saying on United's official website.
"With us having the opportunity to sign Robin van Persie at the time and Chicharito (Javier Hernandez) and Danny Welbeck improving and developing as players, plus Wayne Rooney of course, and then young strikers like [Federico] Macheda, Will Keane, [Joshua] King and Bebe it was difficult to hold on to Michael, also for Michael's own benefit in terms of playing more regularly.
"He's a brilliant professional and a top man and I was disappointed to let him go."
United will host Stoke at Old Trafford in the Premier League on Saturday.