The Office of Fair Trading has confirmed to BBC News Online that investigators have raided the offices of a number of firms involved in the multi-million pound sector.
The probe follows continued complaints from retailers wanting to sell replica shirts at a heavy discount, who said manufacturers have refused to supply them.
And it comes two years after the OFT ended a two-year probe into the industry, amid mounting complaints from fans that they were paying over-the-odds for club shirts.
The inquiry has been ordered under strengthened trade laws which allow the OFT to impose penalties of up to 10% of turnover on firms found guilty of uncompetitive behaviour.
But while confirming that the raids followed initial research into the market, the OFT said it was too early to decide if competition rules had been broken.
"We will not be in a position to decide that until we have the facts," an OFT spokesman told BBC News Online.
JJB denial
Although the OFT has declined to reveal the names of firms raided, sports retail giant JJB Sports has admitted its offices were among those targeted.
JJB, founded by former Blackburn Rovers player David Whelan, said its staff fully co-operated with OFT investigators during last week's raid.
"The directors of JJB advised the OFT that JJB has never been involved in price fixing, of either replica, or indeed any other product, that is sold by JJB," the 420-store chain added in a statement to shareholders.
News of the probe failed to concern investors in the City, where JJB shares ended 1p lower at 409.5p on Wednesday.
'Flood of complaints'
The OFT first targeted the sector four years ago, amid a "flood of complaints" over business practices in the market.
"Retailers told us that manufacturers had threatened to withhold supplies of replica kits if resale prices dropped below a set minimum," former OFT head John Bridgeman said.
"We also have conclusive evidence that some premier league clubs have encouraged manufacturers to prevent discounting.
"I have no doubt that both supporters and parents have been paying artificially high prices."
The OFT closed the probe two years ago, after receiving pledges from clubs and manufacturers that they would not prevent stores from selling shirts at a discount.
Continental imports
Yet even today, shirts typically priced in shops at £40 can cost £7 to make, some industry expert claim.
And retailers such as Tesco, which have sold shirts at a discount, claim they have continued to be denied kit supplies.
Tesco has resorted to buying replica shirts on the Continent, a company spokesman told BBC News Online.
"But we have not able to get enough to meet demand," the spokesman said.
"In the spring we got hold of some Manchester United shirts which we sold for £19.99, compared with £39.99 in most sports shops. As you can imagine, stocks did not last very long."
The firm denied it had made an official complaint to the OFT.