The second-tier side were first handed a six-point deduction in 2021 after admitting to exceeding profit and sustainability limits, while a further suspended six-point penalty was to be applied if the club failed to fulfil an agreed business plan.
On Tuesday, the EFL said Reading had "admitted to the two breaches" of that business plan following a review by an independent panel.
"The club will be required to agree a new budget with the independent Club Financial Reporting Unit for the 2023-24 season aimed at ensuring future compliance with the regulations," the EFL added.
Reading are now 20th in the league standings and just one point above the relegation zone, with seven games left in the season.
In a statement, Reading said they had failed to adhere to the plan "despite radical changes implemented at first team level and right across the structure of the business ... and a rigid adherence to a strict league-monitored wage structure and transfer embargo.
"... as a result, the independent Club Financial Review Panel has been unable to ratify that the club has met its forecast for compliance.
"We have worked closely with the EFL and the independent Club Financial Review Unit throughout the process in our aims to achieve the targets set out in the agreed business plan..."
There was some good news from the club, with Director Mark Bowen stating he was confident that their transfer embargo will be lifted in the summer and no further deductions will follow.
"Through a lot of hard work from our Board - Bryan Stabler, Dayong Pang and myself, we have been able to ensure the business plan meets the Unit’s criteria going forward," he said in an open letter to the fans.
"It has taken time for them to consider this and come back with a ruling – but now we are very confident that this six-point penalty is the last of our medicine and we will now be allowed to come out of the embargo and be able to trade again in the summer."
Reading's next game will be at home to16th-placed Birmingham City on Friday night.
