Carlisle's Brunton Park home was rendered unusable, and they are playing games at three alternative venues.
Coleman was frustrated because Stanley have had two League Two games postponed because of waterlogging.
"Can I start by apologising if I have caused any offence," he said.
In an open letter on the Accrington website he continued: "The quotes published were just a small snippet of a longer interview.
"In that interview, my sympathy for the people who have suffered massively from the floods was made abundantly clear.
"I have no issue with your football club, this was a catastrophic flood and I wish you the best of luck in overcoming the hardship it has caused."
Carlisle have been given a boost in their attempts to restore Brunton Park to a playable state after learning they are eligible to apply for contributions from the Premier League Fans Fund.
Keith Curle's side played the first of their 'home away from home' games at Preston's Deepdale ground last weekend, beating Notts County 3-0 in front of 3,067 fans.
They will also play matches at Blackburn's Ewood Park and Blackpool's Bloomfield Road.
"My main point over this whole affair is that it is now pot luck over whether a team plays Carlisle as an away fixture or on a neutral ground - how can this be fair?" Coleman continued.
"I am not suggesting for one minute that this is favouring Carlisle in the actual game - it clearly favours the opposition, which makes the victory over Notts County even more creditable.
"Could you imagine the league sanctioning the game on 6 February [between the two teams] being played at Ewood Park, which would be tantamount to a home game for us?
"The main benefactors from this whole situation are the possible handful of teams that will not have to face Carlisle United on their home pitch."
National League side Gateshead were forced to play games away from their International Stadium home at the end of the 2012-13 season after their pitch was deemed unsuitable for matches.
They played matches as far afield as Boston in Lincolnshire, Middlesbrough, Hartlepool and coincidentally, Carlisle.
Meanwhile, Carlisle have released striker Kevin Osei, although the former Marseille player only started one of nine appearances for the club.
Accrington Stanley boss John Coleman says he intended no offence to Carlisle United after criticising the Football League's decision to allow them to move home games after flooding in the area.