Sir Bob sparked a heated exchange during a radio interview in which he blamed Mr Cowling for some of the club's troubles and criticised him for not allowing live match commentary on BBC Essex.
Mr Cowling, who recently dismissed U's manager John Ward, responded with a statement on the football club's official site.
Mr Cowling said:
"A few years ago, Bob Russell decided to take a swipe at the way I ran Colchester United and claimed it was just a play thing that I would soon get fed up with and that I was only interested in prawn sandwich eating corporate fans.
"Interestingly, I established at that time that Bob was only attending games if he was receiving a free invite into a prawn sandwich-filled corporate box, and once he was outed as freeloading, prawn sandwich-eating fairweather fan, he stopped coming to games altogether.
"In the meantime, I got on with running the club during four of the most successful seasons in the club's history in terms of league position and Bob found other sources of free lunches.
"Little did I know that he was biding his time so that, after four successful seasons, he could spout a load more nonsense the very first time that Colchester United hit a bad run. So let’s dissect his nonsense.
"In the club’s promotion season from the Conference it averaged 3,381 fans a game and so far this season we have averaged 3,525.
"The following list details the average attendances for the past 28 years and although our gates are currently down by 9 per cent compared to last season, League One gates to date this season are down 10 per cent overall by comparison to last year, so we are very slightly bucking the trend.
"Bob does not have a clue what the break-even point for the Weston Homes Community Stadium is and how could he, because he doesn't have a clue about running a football club."
"Bob is so unfamiliar with Colchester United's recent history that he is unaware that the club’s best ever season was when we finished 10th in the Championship and that was the season after I bought the club...
"Three years after buying the club I honoured the sales contract and offered an agreed price for the remaining shares.
"Because the price was so generous the shareholders who held the largest shares all chose to sell and left me with no other option than to exercise my legal right to mop up the minority of shares that remained so that I could spare the club from unnecessary expense.
"I make no apologies for making sound commercial decisions for the club at a time when so many clubs are close to financial ruin.
"In further response to Bob's points, the BBC offered the club a dramatically reduced fee for live commentary this year and we have improved medical provision for players and fans (working with a local business) and saved nearly 40 per cent in doing so.
"Instead of criticising the way I run my businesses perhaps Bob should be more concerned with the way his political party is being run.
"It was reported on the news that only 16 per cent of the public trust what Nick Clegg tells them and, if I ever get to a stage where only 16 per cent of Colchester United fans trust what I say, then I promise Bob Russell that I will actively seek to sell the club."
Full report and Sir Bob Russell's reaction in Thursday's Gazette.