Charlton have formerly reported Newcastle to the Football League over an allegedly illegal approach for goalkeeper Rob Elliot.
The Irishman, 25, is in the last year of his contract and is understood to be a target of St James' Park boss Alan Pardew, who has loaned Fraser Forster back to Celtic.
But Charlton insist they have not granted Newcastle permission to speak to Elliot and have as a result lodged a formal complaint.
Addicks chairman Michael Slater told his club's official website: "It is well known that Rob is in the last year of his contract, but this does not mean that clubs are entitled to approach and speak to him without our authority.
"At no time did we give Newcastle permission to speak to Rob.
"Having considered the evidence we have received, we are confident that once the governing body investigates the matter, it will conclude that approaches have been made directly and indirectly to Rob and our complaint will be upheld."
Charlton's official action comes in the same week French club Sochaux have claimed to have reported Newcastle to Fifa regarding the Premier League club's pursuit of Modibo Maiga.
Slater added: "We intend to work closely with Sochaux in order to ensure that all facts regarding Newcastle's actions are thoroughly investigated."