Speaking on RTÉ’s Saturday with Colm Ó Mongáin, he said he "never could have imagined" that he would have to give this advice in a country where the migrant experience over the last 20 years has been, for the most part, amazing and welcoming.
"That is now, slowly, unfortunately, changing," he said.
He described how after the violence erupted on Thursday night, he received many messages from Muslims in Ireland who were concerned about videos circulating with anti-migrant rhetoric and calling for violence.
He said the feeling among the Muslim community is if members of the gardaí are not safe, "how will we be safe?"
"We advised our community to be very vigilant. The mosques usually have weekend schools where children go but we asked them to suspend it this weekend. We asked people not to travel to Dublin city, to stay indoors. We asked if they had to travel, not to travel on public transport and don't travel alone."
He said he was shocked by the attack on Thursday outside the school and his thoughts are with the injured children and care worker, adding that the unrest that followed was also shocking.
On Friday morning, the numbers attending Friday prayer in mosques were low and he said many children did not travel to school, particularly those who had to take public transport.
He said this had prompted a meeting online with members of the Muslim community to discuss concerns around safety.
He said the Muslim community understands people in Ireland are upset and angry over certain issues but said "we are all affected by the migrant crisis".
"Unfortunately, anger is being exploited and directed at migrants," he said, adding that people are being wrongly blamed for the crisis or challenges the country is facing.
He said that ideology is dividing the community and it is "very dangerous".
He said more engagement and interaction is needed and more participation in civic life, starting by having the 12% of migrants here represented in the Dáil and Irish life.
He said the events of this week have motivated all of them to think seriously about this.
Speaking on the same programme, Labour Party leader Ivana Bacik said it is "really sad" to hear the Muslim community are being advised to stay away from Dublin city centre for their own safety.
"It is appalling to hear that about our own capital city, that people feel so unsafe. And I think the government's approach and that response of 'nothing to see here, we have enough resources’, that simply has a very hollow ring to it for anyone who watched or experienced the horrors of Thursday night."
She said there needs to be a greater urgency in seeing sufficient numbers of gardaí on the streets, adding that she wrote to the Garda Commissioner months ago to highlight a lack of resourcing of community policing.
Minister of State Kieran O’Donnell said he regrets that members of the Muslim community feel they are unsafe.
"We want to provide that level of security so they can go about their daily lives."
He said the message is loud and clear that the Government is strong on law and order to ensure anyone who lives here regardless of where they come from or creed, is safe.
He also said there is very strong support for the Minister for Justice and the Garda Commissioner.
He said they want all political parties to unite together on this issue to deal with the "thuggery" that happened on Thursday night.
He said it is "incumbent" on all parties to unite on this matter and work with government.
He also said in the aftermath of the riots, gardaí will have four public order units in Dublin throughout the weekend which will bring "great security" to people.
"They are very much on top of this," he said.