The Refugee Council has written to the Commons Speaker urging him to ask MPs not to identify hotels to protect the safety of those staying there.
But several Tories said they would still "name and shame" hotels getting taxpayer money to house migrants.
The UK spends almost £7m a day on hotels for asylum seekers and refugees.
Last month an immigration processing centre in Dover, Kent, was firebombed in an attack police have said was motivated by extreme right-wing terrorist ideology.
In the Refugee Council letter, first reported by the Guardian, the charity's chief executive Enver Soloman said the "horrific" incident highlighted how asylum seekers were vulnerable to violent attacks by extremists.
"It has been Home Office practice to not publicly name hotels where people are staying in order to guard their safety and privacy, but we know that increasingly MPs are naming specific premises when they raise this issue," he wrote.
"It is of course right that MPs should be able to raise any constituency issue in Parliament, but this can be done without identifying a specific hotel and potentially making it more vulnerable to attack."
Campaign group Hope Not Hate said it had recorded 182 visits from anti-immigration activists to migrant accommodation sites so far this year, some of which involved asylum seekers and security staff being harassed and filmed.
However, Tory MP Lee Anderson, who represents Ashfield, wrote on Facebook: "Like many of you, I am sick and tired of seeing our hospitality abused and people who are simply economic migrants cheating our system via small boats and dodgy human rights legislation.
"I will not be silenced and will name and shame these greedy hotel owners."
Brendan Clarke-Smith, Tory MP for Bassetlaw, said he would always be "welcoming to those in genuine need" but posted a similar message, saying: "I will not be silenced and will use the privileges given to me as a Member of Parliament to continue to speak out on this issue."
Former Conservative minister David Davis has also raised concerns about plans to house asylum seekers at a specific hotel in his constituency of Haltemprice and Howden, as well as another which is already being used for the purpose.