Speaking to the media in Delhi, the actress-turned-politician said Banerjee should have initiated measures to stop the practice much earlier.
"Didi has taken steps now, that's fine. But there will be more chaos on returning cut money. Because a person who has taken it directly, he is only the front man. There are others who are behind the wings. They have also taken their share. So the money has to be returned according to this chain.
"This money should be returned. But the amount which has reached somebody's home already, it is difficult to get that money back," Roy said in explosive comments on the issue.
Addressing party workers earlier this week, Trinamool supremo Banerjee lashed out at those leaders taking cut money or commission from beneficiaries of government schemes, and ordered them to return the ill-gotten amount to the public from whom they had taken it in the first place.
Roy, however, cautioned that Banerjee should ensure that it should not lead to the situation where those who take small amounts of "one or two per cent" are reined in, but the shares of those taking higher percentages go up.
"Those who could not get the cut money earlier, will nag those who took it to return the money. There is chance of trouble. Didi (elder sister, as Banerjee is affectionately called) should look into this.
"It should not be the case that those who were taking one per cent or two per cent of the total amount of schemes are reined in, but simultaneously shares of those who now take bigger amounts go up. This will only sow confusion in the party.
"If there is a situation where only a handful gets the cut money, and the majority don't, that is also not proper," she said.
( With inputs from IANS )