The ACC had threatened the move last week after sending a letter to Sierra Leone Football Association (SLFA) president Isha Johansen, telling her to step down over allegations of match-fixing involving the national team.
Johansen and her secretary general Chris Kamara have been banned from the SLFA offices by ACC officials, but the remainder of the staff have been allowed to continue their work.
Both deny they have done anything wrong.
"Staff at the SLFA offices have been warned not to have any business with Johansen and Kamara and not to allow them into the secretariat," ACC official Alhassan Kargbo told BBC Sport.
"Anyone who goes against the orders will face the law."
FIFA said earlier this week that they were monitoring the situation in the country and are likely to view the forced removal of Johansen as government interference in football affairs, especially as they are conducting their own investigation into the match-fixing allegations.
FIFA are looking at matches as far back as a World Cup qualifier against South Africa in 2008, while they are also chairing negotiations between the Sierra Leone sports ministry, SLFA officials and various other stakeholders over delays to football association elections.
The delays have been caused by a number of factors, including a resistance to integrity checks that FIFA wants carried out on those who intend to stand for positions.
Johansen, who intends to stand for re-election, was briefly detained in 2016 over alleged graft but was released without charge and also survived being ousted by the SLFA executive committee last year as FIFA refused to recognise the move.
She claims to have received numerous death threats in recent years but is determined to stand again for the post of president when elections eventually take place.
"I have been called all kinds of vulgar names ... received so many death threats ... but I haven't entertained such abuse,” Johansen told Reuters last year.
"I want to be a pioneer for good governance, gender equality and inclusivity in football, to make a difference in a man's game."
(Reporting by Nick Said; Editing by Hugh Lawson)
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