The message, which reads "Up the RA", appeared on Duffy's @ShaneDuffy34 account on St Patrick's Day.
However the Co Londonderry man said someone else had taken his phone and sent the tweet.
Apologising, Duffy wrote: "sorry everyone some little paddy had my phone last night tweets wernt me.. sorry if it offended anyone!! cant leave ur phone anywhere now!!"
The 21-year-old said he has received "so much hate" over the incident.
He continued: "Can't do much more ino it's offended alot of people getting alot of hate for something I didn't do. For to much to lose for tweeting... Something like that. The retweets and tweets was not me. Got to accept the hate. Really am sorry for this mess! Sorry guys!"
Duffy, who plays for Everton in the Premier League, represented Northern Ireland at junior level before switching allegiances to the Republic.
The Twitter controversy comes after fellow Derry footballer James McClean came in for criticism last month when he tweeted that his favourite song is Broad Black Brimmer by the Wolfe Tones, which is about a young boy whose IRA man father died before he was born.