Islam is often "misunderstood, misinterpreted and misrepresented", according to Communities Minister Malcolm Chisholm.
Glasgow Central Mosque where Mr Chisholm addressed Muslims
At the launch of Islam Awareness Week in Glasgow Central Mosque, he reiterated the Scottish Executive's belief in religious diversity.
Mr Chisholm said anti-Islamic comments or abuse would not be tolerated.
During the speech, he revealed that First Minister Jack McConnell hoped to meet imams across Scotland.
"Recent events have unfortunately prompted some in our communities to believe that it is justified to make anti-Islamic comments or to abuse or harass Muslims, or those they presume to be Muslims, in the street or other places," he said.
"I deplore that and can assure you that such views and behaviour have no place in Scotland."
Mr Chisholm's speech follows comments made by former home secretary Jack Straw about Muslim women wearing the veil.
The Leader of the Commons described the veil as a "visible statement of separation" and a barrier to communication, sparking debate throughout the country.
Mr Chisholm said it was not an issue in Scotland.
"We are absolutely clear about this in Scotland - we cherish and believe in diversity," he said.
He praised the 13th Islam Awareness Week, which involves a series of events throughout the country aimed at promoting understanding of the religion, for playing a key role in breaking down barriers.