Tottenham forward Gareth Bale scooped both the main award and young player honour last month, before adding the Football Writers' prize as well.
For the prestigious FWA honour, members could vote virtually until the result was confirmed.
Yet the players have to vote much earlier, which Ferdinand feels leads to an inadequate conclusion.
"The problem with the PFA awards is that the voting system is flawed," Ferdinand told Manchester United's oficial website.
"There's so much technology at hand that you could do it over an iPad and just say 'bang, bang, bang' at the end of the season.
"I am not just being biased but if it was voted for today Robin van Persie would win it by a country mile.
"But it was voted for by the players in late February or March.
"Gareth Bale is a worthy winner, but for me it isn't a true reflection of the season."
Both United boss Sir Alex Ferguson and Manchester City counterpart Roberto Mancini are in agreement that Van Persie's Old Trafford arrival from Arsenal made the significant difference this term.
The question now is who Ferguson will add to his squad this summer.
Not that the entire position around the United manager is straightforward.
Whilst it has been confirmed the United manager will have hip surgery in the summer, no explanation has been put forward why the 71-year-old's operation will take place after the club's summer tour to Australia and the Far East rather than immediately, when it would have no impact on any club business.
There is also the strange matter of a massive gamble on David Moyes to become next United manager amid reports that he will be announced as Ferguson's assistant in the summer.
Moyes is out of contract at Everton in the summer and has been cagey about revealing his plans.
Yet within this uncertainty, there were Ferguson's programmes notes ahead of Sunday's defeat to Chelsea, when he stressed he was going nowhere.
"This team of champions is not going away - we are here for the long ride," Ferguson told United Review.
"We will get better and if we apply ourselves in our normal fashion I see our 20th league title as nothing but the start of another decade of success.
"Whether I will be here to oversee another decade of success remains to be seen, but I certainly don't have any plans at the moment to walk away from what I believe will be something special and worth being around to see."
Ferguson has been around for so long, it is hard to imagine United existing without him, although that day must come soon, even if it is not in his immediate plans.
Certainly, veteran midfielder Ryan Giggs anticipates the Scot further strengthening his squad this summer, rather than considering his future.
"I don't expect many changes but the manager looks to strengthen where he can, whether we have lost a league or won it," Giggs told SiriusXM FC.
"He never stands still. He always wants to better the team.
"If that is bringing in one player, or bringing in two or three, he will assess with his staff.
"One of the manager's skills is that we tend to be one step ahead. He always looks to the next challenge.
"I am sure there will be a couple of players at least coming in.
"But we already have a good, young squad and a mix of experience and young players."