Peter Robinson told the Irish News on Wednesday he would not trust Muslims involved in violence or devotees of Sharia law.
The DUP leader has since said he didn’t want to “cause distress” to Muslims.
However, businessmen Phillip O’Doherty and Martin Symington have said the comments could have a negative impact.
Mr Robinson made his comments in defence of Belfast pastor James McConnell, who had described Islam as “heathen” and “satanic”, and said he did not trust Muslims.
Mr O’Doherty, who employs hundreds of Muslims, described Mr Robinson’s comments as “very dangerous”.
Mr O’Doherty, from Londonderry, owns E&I Engineering near Dubai and has been invited by Invest Northern Ireland to go on a trade mission to the Middle East.
“I was quite shocked that he (Peter Robinson) got involved at all,” Mr O’Doherty told BBC Radio Foyle.
“The comments are very poor and very dangerous.
“The bulk of our employees are mainly Muslims and we find them very trustworthy. They will hear about these comments and will be baffled.