In a letter, David Bowers wrote that Syrian refugees should not be resettled in his city, citing security concerns.
To highlight the point, he compared the concern over the refugees to the 1940s internment of Japanese Americans.
The internment camps - now considered illegal - are widely considered to be an embarrassing period in US history.
"I'm reminded that President Franklin D Roosevelt felt compelled to sequester Japanese foreign nationals after the bombing of Pearl Harbor and it appears that threat of harm to America from [IS] now is just as real and serious as that from our enemies then," Mr Bowers, a Democrat, wrote.
More than 30 US governors have said they do not want Syria refugees resettled in their states after recent attacks in Paris tied to the so-called Islamic State killed more than 100 people.
Although the governors do not have the legal authority to do so, they can complicate the resettlement process. US President Barack Obama called their response "hysterical".
Virginia Republicans sought to distance themselves from Mr Bowers' remarks.
"Comparing the prudent step of pausing to evaluate a vetting processes to the unconstitutional internment of American citizens proves that Democrats simply don't understand national security," John Whitbeck, the chairman of the Virginia Republican Party, said in a statement.
The letter drew also ridicule on social media with celebrities condemning Mr Bowers.
Actor and Japanese-American George Takei wrote on Facebook: "Mayor Bowers, there are a few key points of history you seem to have missed."
"The internment [not a "sequester"] was not of Japanese "foreign nationals," but of Japanese Americans, two-thirds of whom were US citizens," Mr Takei wrote.
"I was one of them, and my family and I spent four years in prison camps because we happened to look like the people who bombed Pearl Harbour. It is my life's mission to never let such a thing happen again in America."

The 33-year-old, who made 27 Premier League appearances for the Canaries in 2015-16, has signed a two-year deal.
The former Middlesbrough and West Ham United man, who began his career at Portsmouth, has won promotion from the Championship with four different clubs.
"Gary is a really good signing for us, who adds everything we need to our midfield," head coach Lee Johnson said.
"He may have just turned 33, but he's still fully mobile and very fit. He's a really good decision maker who can be a coach's eyes and ears on the pitch."
O'Neil helped QPR to promotion via the play-offs before his move to Norwich in 2014 and has played more than 200 top-flight games.
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The mayor of Roanoke, Virginia, has come under criticism after he appeared to endorse the internment of Japanese Americans during World War Two.
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Bristol City have signed midfielder Gary O'Neil on a free transfer from recently relegated Norwich City.