Shay Given missed training on Tuesday morning as he underwent treatment for a stiff neck.
Republic of Ireland assistant manager Marco Tardelli is hopeful though that Given's injury is not too serious.
He told Sky Sports News: "He has a little problem in the neck and in the back. But I think that tomorrow is maybe possible for him to train."
Richard Dunne, Keith Andrews and Keith Fahey also sat out training in Malahide.
Dunne and Fahey were both having treatment for minor injuries, while Andrews was simply rested.
Tardelli added: "Fahey should hopefully be fit and no problem for Estonia on Friday."
Millwall's David Forde will definitely miss the game, however, and has returned to his club for treatment on a thigh injury.
Motherwell's Darren Randolph has been called up as a replacement.
Robbie Keane did train, despite travelling from the USA after playing and scoring in LA Galaxy's 3-1 MLS Cup Final win over Real Salt Lake.
Tardelli said: "I told him not to train and to rest, but he wanted to train. I watched the game and he seemed in good form. It is good because without Doyle and Best and Long we needed a striker for Friday."