The Irrawaddy saw its main English-language website briefly replaced with a black screen and notice railing against a blog it ran in Burmese about Myanmar nationalist cleric Wirathu's weekend meeting with controversial Buddhist monks in Sri Lanka.
The Buddhist-majority countries have seen rising religious hate speech and attacks on minority Muslims, with some hardline monks accused of fanning intolerance by stoking fears of a threat from Islamic jihadists.
The hackers claimed the Irrawaddy "supports jihad and radical Muslims" and was "attacking Buddhism with so called freedom of speech".
Their notice, which was later taken down, appeared to come from Sri Lanka and demanded the publication apologise for referring to the country's hardline Bodu Bala Sena (BBS) or Buddhist Force as "radical".
The cyber attack is the latest in a string of hacks for the Irrawaddy, which operated for years during junta rule as an exile media group based in Thailand but now also has an office in Myanmar's commercial centre Yangon.
Editor Aung Zaw described the attack as "brutal", but said the website was being repaired.
He said the Irrawaddy Facebook pages had been inundated with hate mail in recent days linked to coverage including the anniversary of Myanmar's junta crackdown on 2007 monk-led protests.
"It is very clear that a team is behind the cyber attacks and cyber abuse... Clearly, they are criminals," he told AFP.
Myanmar was gripped by harsh military rule for decades until a quasi-civilian regime took power in 2011, implementing reforms that have opened the country to the world and raised hopes of a transition to democracy.
But the country has also suffered several bouts of religious violence since 2012 that have left over 200 people dead and tens of thousands displaced, mainly Muslims.
Sri Lanka and Myanmar share a common Buddhist heritage and have close cultural ties.
The link between Wirathu and BBS has caused concern, with the Muslim Council of Sri Lanka warning the Myanmar monk's visit last Sunday posed "a serious threat to peace in our beloved motherland".
Sri Lanka suffered its worst religious violence in decades in June when riots broke out in the resorts of Aluthgama and Beruwala, leaving four people dead.
The BBS has been accused of instigating the attacks, a charge it denies.
"The incident is unfortunate ... we wanted to make sure there is no such thing as home advantage, an event for all Asians to become one," Son said.
"It is unfortunate it happened when a South Korean athlete was involved.
"I checked and there was no South Korean judge but of course there can still be claims of home advantage. But we tried to make sure there was no such thing."
Devi's medal was left on the podium after the ceremony and Son said a working group of the Olympic Council of Asia (OCA) would decide if it would be returned. However, he also said the athlete's wishes in regards to the medal could be respected.
On Wednesday the International Boxing Association AIBA said it would open disciplinary proceedings against Devi for her behaviour.
"The whole incident looked like a well planned scenario by her and her team, and it is regretful to watch a boxer refuse the medal regardless of what happened in the competition," said David Francis, the AIBA technical delegate at the Games.
"In this regard, as the technical delegate, I had to request OCA to review this incident, so any boxer or athlete in other sports will not follow in her footsteps by respecting the spirit of fair-play and sportsmanship of the Olympic movement."