"It's very easy to stereotype people on the margins - we see that throughout history, we're seeing it again these days.
"It's very easy to stereotype the poor and label them as one particular class without knowing their stories.''
Farrelly said the Mission's staff knew many of the city's homeless and worked to help them every day.
"We do have homeless on the streets of Auckland. We know these people. We know where they live and where they hang out.
"The City Mission goes on the streets every morning at 6 o'clock and actually physically connects with our homeless.''
Sir Bob's comments included that he could not believe there were beggars in New Zealand still.
"They're a bloody disgrace. They're an eyesore. It's a disgrace in a modern society that fat people - that fat Maoris as they mostly are - are lying on our streets of our city, begging,'' he said.
"I was in the city yesterday, in Wellington, and one bugger was standing there. One bugger was standing there - he had a message, this Maori bloke: 'I'm not on welfare', and this apparently was an achievement: 'So give me money'.''
In an email to the NZ Herald today, Jones made clear he was referring to beggars, not homeless people, as reported in the Herald's headline last night. The Herald regrets this error and apologises to Jones.
Farrelly said it was often difficult to distinguish who was a genuinely homeless person and a person who did have a home, but was out on the streets begging for money.
His advice to the public was not to give them any money, unless they were buskers.
"By all means, engage with them - have a cup of coffee, have a chat. Advise them to go to a place like City Mission to get some help."
Meanwhile, Herald readers have also reacted to Sir Bob's comments; some labelling them racist and disappointing.
In a Herald online poll, readers were asked: "Do you think begging should be made illegal?''
By 9.30am, more than 34,000 voters had submitted answered yes, no or I don't mind.
A total of 73 per cent of people said yes, 20 per cent answered no, and 7 per cent said they did not mind.
Mary-Jane Shepherd said: "As a Maori New Zealander, I am saddened and disappointed to hear yet another public example of casual racism by a prominent New Zealander.
"It concerns me that men who are looked up to by the public and have earned the privilege of being knighted speak so cruelly and spitefully of Maori people. Sir Bob talks of [beggars] being fat Maori who are uneducated and yet provides no hard evidence for us when making such a provocative statement.
"These words of Sir Bob's hurt me and hurt my people. They hurt all of us.''
John Henry, of Rotorua, acknowledged it was unnecessary to bring ethnicity into the conversation.
"I think Sir Bob is wrong to stereotype [beggars]. They have complex needs and their situations will vary.
"Nothing to do with race or how one looks.''
Heeni Phillips-Williams said the comments were outrageous.
"One has to feel sorry for Sir Bob Jones given his latest attack on [beggars] being fat and Maori.
Another disappointed reader simply wrote: "Is he really a sir?''
Others, however, agreed with the comments; acknowledging there was a big problem when it came to beggars.
Steve Bannister wrote: "They are an eyesore - and what about the rights of the people they harass?
"You see them going after particularly vulnerable people around ATMs. Even to the extent that the small local shopping area has employed security guards to protect shoppers from the quite aggressive beggars.''
Dave Winfield also praised Sir Bob's comments, saying: "It's about time this was said. Beggars are on welfare and they do not have to annoy people who have already paid for them in their taxes.''
