Only 44 out of 92 clubs currently have both their 2022-23 season kits on sale.
Premier League clubs including Crystal Palace and Leeds United are among those who have neither kit available.
Some have blamed the delays on disruption and factory shutdowns in Asia due to Covid.
It means some clubs won't have their new kit on sale before the season starts, which for the Championship is 29 July, for League One and League Two is 30 July and for the Premier League is 5 August.
Out of the 92 clubs in the top four leagues:
44 teams have both kits available for sale on their website
22 teams have only their home kit available
7 teams have only their away kit available
19 teams have neither kit available
One English Football League chief executive, who did not want to be named, told the BBC his club had signed off kit designs in October, with orders placed shortly afterwards, but neither their new home or away kit were available to sell yet due to Covid disruption at factories in Asia.
He said it was difficult to quantify the cost to the club until it saw the impact on sales, but added that some clubs would face a financial hit.
"We can manage our cash flow, but it will impact on some clubs' cash flow, I'm sure, because July is a month when there's not much cash coming into the business," he said.
"We're in a position where that hasn't caused any disasters for us. But for some clubs I would imagine it's pretty difficult."
He added that the delay would also be disappointing for fans.
"If you're a parent or a grandparent who's going to buy a kit for a young child's birthday in July, which you would normally have done, you've not been able to do that, you've got to wait," he said.
Sandy Domingos-Shipley has three children, aged 15, 13 and eight, who are all Leeds United supporters.
Normally she would buy them the new kit as soon as it was released before the start of the season but this year she hasn't been able to, with the club saying it won't be on sale until late August.
Although Sandy said she would still be buying the kit when it was available, she added: "The season will be four weeks in and for the kids it kind of ruined the moment because it became our own tradition.
"It makes no sense because that's when you know that you're gonna get lots of people to buy."
Manufacturer Adidas said: "Like many other industries, we continue to be confronted with limited port and transport capacities.
"We understand the frustration felt by the fans at this time and we have worked in close collaboration with our club partners to find the best solution on delivering the product as soon we can."
Leeds United did not respond to a request for comment.
Kieran Maguire, a senior lecturer in football finance at the University of Liverpool, said some clubs were being affected by the impact of Covid in Asia, where many factories are based, with production limited due to restrictions.
He said a shortage of container ships and disruption at ports was also contributing to the issue.
However, he told the BBC the financial impact on most elite clubs would be limited as they are generally paid a fixed amount by manufacturers for the season, with only around 7% commission per unit sold.
"I think fans are fairly sanguine in relation to this," he said, adding that fans who wanted the kit would still buy it when it was available.
Mr Maguire added that the other peak market for clubs was Christmas and the issue should be resolved by then.
He said smaller clubs were more likely to be affected, as manufacturers would prioritise bigger clubs who sell more shirts.