In the article in Investigate magazine, Mr Prosser said while he accepted most Muslims were not terrorists, it was "undeniable" that "most terrorists are Muslims".
His column was sparked by the confiscation of his pocket knife before boarding a domestic flight and he wrote that New Zealanders' rights were being "denigrated by a sorry pack of misogynist troglodytes from Wogistan, threatening our way of life and security of travel in the name of their stone age religion, its barbaric attitudes towards women, democracy, and individual choice".
"If you are a young male, aged between say about 19 and about 35, and you're a Muslim, or you look like a Muslim, or you come from a Muslim country, then you are not welcome to travel on any of the West's airlines," he wrote.
He told Radio New Zealand's Nine to Noon this morning he had not calculated the percentage of young Muslim men who were involved in terrorism compared to the global Muslim population.
Mr Prosser said he should have called for an investigation into the merits of racial profiling, instead of calling for a blanket ban on young Muslim men being able to fly on Western airlines.
Mr Prosser said it was silly to ignore something which was an apparent threat on the basis of not wanting to offend.
"It's a reality that because of the actions of a very small few, the entire world has had to change the way it behaves even though the vast majority of the people who travel are not going to cause any problems on aeroplanes."
He wouldn't stand down as an MP, and denied he was a racist.
"Islam is a religion, it's not a race. I don't know why people jump on the racist bandwagon."
Mr Prosser said he realised he had given cause for people to be offended "where they don't fit that profile where the vast majority of peaceful, law-abiding Muslims weren't sufficiently separated.
"I didn't have balance in that article. For that I'm sorry."
He later released a statement which read:
"Terrorism and airline safety worldwide is a serious issue which consumes great resources and causes major disruption.
"The issue requires positive solutions, and my article in Investigate magazine sadly did not contribute to that.
"I accept that I impugned many peaceful law-abiding Muslims, and to them I unreservedly apologise.
"My opinion piece does not reflect the views of the New Zealand First Party and I deeply regret any embarrassment caused by it."
Mr Prosser told Radio New Zealand he considered himself a "shock jock with a pen" but said his language in the column was not appropriate.
"Having had time to have some conversations yesterday with Winston [Peters] and a couple of others, and having had time to reflect on it overnight, I concede that some of the language that I used in the column wasn't appropriate.
"There's a style that I've developed over the previous 10 years to coming into Parliament, which is sort of 'shock jock with a pen', that even though I've gone to some lengths to try to separate my role as a columnist from my role as an MP, I can see now that it's not appropriate for me to be saying things in the way that I have said them anymore.
"The article wasn't balanced in the sense that I did say not all Muslims are terrorists, but I didn't go any further beyond that, and I should have gone to greater lengths to reiterate that we're only talking about a very small, extremist minority.
"I didn't have the balance in there that would enable a reader to separate the fact that the majority of Muslims are law-abiding people. And that's obviously caused some upset, and for that I'm sorry."
Meanwhile, Investigate's editor Ian Wishart said he only "skimmed" over the article before it went to print.
"I perhaps should have read it more carefully," Mr Wishart told Morning Report.
"I probably would have gone back to him said, 'Do you really want to say this in that way?'
"The point that he was making ... that there is a valid argument to be made about the amount of wasted time and money in profiling people at the airport and taking aside grandmas and babies for security."
Mr Wishart criticised the media for not publishing the column in its entirety and the comments about not letting Muslims on Western airline flights were being taken out of context.
"It's a ridiculous remark but in the context of the column it's a tongue-in-cheek remark," he said.
Mr Wishart said the column raised important issues about the Muslim extremists entering New Zealand.
"I would not have phrased it in the way that he's phrased it and I think, I don't know what Richard Prosser thinks, but he's probably and saying, 'Maybe I shouldn't have phrased it that way myself'."
By last night the story had spread as far as the United States, the United Kingdom and Malaysia. At least two Australian media outlets were running Mr Prosser's comments as well as the Straits Times in Singapore and The Muslim News, a UK-based news website.
The Sun Daily in Malaysia had as its lead headline, 'New Zealand lawmaker calls for Muslim Flight Ban'.
ABC in the US was reporting: "NZ politician wants Muslims banned from airlines".
Mr Prosser's comments have been slammed by politicians across the political spectrum, however NZ First Leader Winston Peters said there was an "element of truth" to Mr Prosser's comments and did not believe the MP should apologise.
British MP George Galloway, who has campaigned against Islamophobia for 30 years, told Radio New Zealand Mr Prosser's comments were "disgusting".
"I'm surprised because it's New Zealand and I'm surprised that it has come from the pen of a Member of Parliament.
"It's not surprising in another sense that there are right-wing politicians across the world seeking to scrape the barrel of prejudice in order to boost their political popularity."
Mr Galloway said it was "deeply shocking" that Prosser's party leader had not repudiated his comments entirely.
"What kind of leader would not see that talking about 'Wogistan', talking about Muslims - 1.7 billion of them - in these sweeping stereotypical and deeply insulting ways [is wrong]?
Mr Galloway said the comments could be "dangerous" for New Zealand.
"It's not good for New Zealand to be known as a country where Parliamentarians go un-repudiated when making these deeply racist comments."