The striker was suspended by the League One club last week after a "breach of discipline" and will not be allowed to play until the inquiry is over.
On Wednesday, the 25-year-old admitted an online banking fraud, but the suspension is believed to be unrelated.
It is expected the investigation will be concluded by the end of January.
"The club does not wish to pre-judge the circumstances and awaits the outcome of the Football Association's review and assessment before the club makes its own decision surrounding Nile's future," a club statement said.
"The club recognises the difficulties Nile Ranger has suffered in the past and, although to a lesser extent, that continues to impact on the present.
"It is therefore fair that the club comes to a decision only when all the facts, and factors, are to hand.
"A negative decision, and consequential termination of Nile's contract, would effectively undo all the good work the club, manager Phil Brown and his team mates have achieved to date. However, no player is more important than the club."
Southend United say they will not make a decision on Nile Ranger's future at the club until a Football Association investigation is completed.