Fryers came through United's academy and made six appearances for the Old Trafford outfit. However, he refused to sign a long-term contract, allowing Tottenham to step in.
Yet the anticipated deal failed to materialise last summer as the Premier League rivals were unable to agree a compensation package.
It left Fryers free to sign for any club in Europe for no fee and he subsequently joined Belgian outfit Standard Liege on a two-year deal in August.
However, it has come as no surprise to Ferguson that Fryers should now join Tottenham at the first available opportunity, and he is not happy about it.
"I am disappointed in Tottenham," said Ferguson.
"It is a blatant manipulation of the situation. They tried to buy him from us at the end of last season but we couldn't agree terms. Then they took him on trial, came back from Portugal and said they couldn't afford him.
"All of a sudden he signed for Standard Liege but I expected him to go to Tottenham in the January window.
"The league should look into it. They should stop the registration until they examine it. There will be a trail. Either mobile phones or something. It is obvious to me."
Tottenham defended the deal they had agreed with Fryers, with a club spokesman saying: "Zeki Fryers was out of contract in the summer. We had looked in to the possibility of signing the player but were unable to agree a deal on the terms Manchester United were asking.
"Zeki chose to go to Standard Liege, who paid compensation to Manchester United. Zeki enjoyed his time at Standard. However, when Standard sacked their manager in November Zeki wasn't part of the new manager's plans, which he accepts and understands happens in football.
"Unfortunately, a combination of this, and the fact that he had become homesick meant he wanted to return to England and his representatives made contact with clubs in England. This afforded us a second opportunity to sign the player and as per FIFA's solidarity contribution mechanism, Manchester United will receive five per cent of the transfer fee we have paid."
A statement on the Belgian club's website on Friday night read: "The young defender felt homesick and had difficulty acclimating to life away from home and family.
"So when the London club became interested we understood the situation and were not opposed to the return of the player in England."