The paper was swept up in the rising anti-Muslim tide in the US in the run up to the ninth anniversary of 9/11at the weekend.
The Portland Press Herald's story, "was quickly followed by Connor said the paper "sincerely" apologised for offending "many readers" and said the paper "erred" by not offering balance to the story and its prominent position on the front page.
Connor wrote: "In hindsight, it is clear that we should have handled this differently and with greater sensitivity toward the painful memories stirred by the anniversary of 9/11."
He said readers began writing to the paper and website en masse, criticising its decision to cover local Muslim Ramadan celebrations so prominently.
The paper used social media to respond and it posted its answers to readers on Facebook, Twitter and on its own website.
The paper said: "A good eight hours into the day, our editors were still working from home to keep up with a necessary response to our customers.
"Some managers came to the office on what was supposed to be a day off."
The apology was attacked by some bloggers, with Minnesota blog The Meat Raffle calling
The Meat Raffle said: "Unfortunately what Connor's done is created a self-inflicted wound to his newspaper. By apologizing for a factual story portraying part of the community it covers, the Press Herald has damaged its ability to educate, betrayed the journalists who work there, alienated a part of their audience and shown that editorial control can be won by the power of the mob."
The 9/11 anniversary has seen levels of anti-Muslim sentiment in the US reach fever pitch. A bitter argument around plans to build a Muslim cultural centre and mosque near Ground Zero is at the heart of the dispute.
The Ground Zero cultural centre has sparked a debate across the US that was pushed to incendiary levels by who threatened to burn hundreds of copies of the Koran.
He eventually backed down, but not before adding heat to the raging mosque debate and fuelling rival demonstrations over the anniversary weekend.
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