The 20-year-old looked set to join Spurs when his contract at Old Trafford expired on June 30 but the two clubs were unable to agree a compensation package.
Fryers instead moved to Liege on a two-year deal, meaning compensation did not have to be paid to United, and ended his spell in Belgium to sign for Tottenham on Thursday.
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"How would you put it? To me, I think it's a blatant manipulation of the rules," he told MUTV.
The United boss added: "I think the league should look into it.
"I think the registration should be stopped until they investigate it thoroughly. There's bound to be a trail, either mobile phones or e-mails, that could give you the full story of it.
"I must say I'm disappointed in Tottenham. For whatever reason, a club that size has decided to go down this route. I'm disappointed."
Fryers initially joined up with Spurs on trial after his contract at United came to an end, even taking part in a pre-season training camp in Portugal.
Sir Alex added: "We knew immediately and suspected that he would return to Tottenham in January and that's happened. It's a Daniel Levy deal. You know, it's his fingerprints all over it. It's the kind of thing we expected he was going to do."
Tottenham have refuted the Scot's suggestions, though, insisting Fryers was "homesick" and wanted to return to England.
A Spurs spokesman said: "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."