The punishment, which is understood to have been applied to 10 Championship clubs this year, was for filing their 2019-20 accounts late.
They were due in March, but that was the month the Owls finally published their 2018-19 figures.
The Government gave company an extra three months to file their 2018-19 accounts because of the Covid-19 pandemic, and Wednesday delayed again to take account of their case for breaching financial fair play rules, which saw them docked six points. The issue was partly over when they accounted for the sale and lease back of their Hillsborough home to club owner Dejphon Chansiri and because it was decided they were not allowed to book it when they did, before the transaction was completed, they were able to include the first £7.5m instalment in their 2019-20 figures instead.
But that case was resolved in November, when the guilty verdict stood but the initial 12-point penalty was halved.
Companies House allows accounts to be filed in April this year because of the knock-on effects, but the Football League has stuck to its March deadline.
Relegation-threatened Wednesday, who have been placed under embargoes before, are understood to be confident of having it lifted in time to do business in the summer. With the number of first-team players out of contract in double figures, they will need to be active in the transfer market regardless of whether they are in the Championship or League One.
Huddersfield Town are thought to have been one of the clubs placed under embargo, but to have since come out of it.
The Terriers signed Oumar Niasse as a free agent on March 26, their second signing outside the transfer window after also picking up free agent Yaya Sanogo on February 24.
Wednesday took two former Premier League players on trial in March – former Sheffield United and Middlesbrough player Ravel Morrison and Manchester United product Danny Simpson who was at Huddersfield last season – without signing either.
Although the Football League does not announce which clubs are under transfer embargo, Birmingham City, Blackburn Rovers, Cardiff City, Derby County, Reading and Stoke City are believed to have befallen the same fate. Coventry City and Luton Town have confirmed their embargoes.
The Owls were under embargo in the summer of 2018, and had a “soft” embargo, where deals needed extra League approval, under Steve Bruce.
Wednesday are six points from safety in the Championship with seven games remaining, but gave their survival prospects a time boost with a 5-0 win over Cardiff City on Easter Monday.
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