Police are preparing for a protest outside Maghaberry Prison supporting dissident republicans who are refusing food.
Justice Minister Naomi Long said inmates had taken the action in response to the removal of a prisoner for medical treatment who went through the normal coronavirus-checking procedure of entering isolation on his return.
She said: “We put the safety of our prisoners and prison staff at the forefront of all we do.
“It is hugely important that we keep Covid out of the prison.”
She said 1,000 prisoners had gone through the admission process. Only one has tested positive.
Ms Long told the Assembly she was aware of a demonstration to be held outside the Co Antrim high-security prison on Saturday.
“We have been liaising with the PSNI (Police Service of Northern Ireland) to ensure that is handled in an appropriate way.
“The focus will be on ensuring public order and life is protected throughout all stages of any protest.”
Former Ulster Unionist leader Mike Nesbitt said a minister whose calling card was ending division was presiding over a separated regime for republican prisoners.
She said: “The current arrangements on separation lies with the Northern Ireland Office and Secretary of State.
“My duty is to ensure that prisoners’ wishes are respected and that the Prison Service does its job.
“It is not my duty to direct the Secretary of State.”
The minister also condemned a threat made against Ulster Unionist Assembly member Doug Beattie by the UDA.
She said it was unacceptable to subject someone to intimidation for speaking their mind and standing up for the rule of law.
UUP leader Steve Aiken said: “The threats made against Doug Beattie by the South East Antrim UDA are absolutely reprehensible.
“That any criminal organisation thinks that it can interfere with the process of democracy is unbelievable, but for a public representative like Doug who has steadfastly stood up to violence and intimidation from all sectors across the globe, just underlines what a disgrace they are.”
Ms Long answered questions at Stormont on Tuesday.
She also expressed concern about the potential to “seriously compromise” Europe-wide investigations after Brexit.
“It is a hugely important issue and a highly serious one.
“We could end up in the situation where European arrest warrants have to be negotiated in bilateral agreements with each country.”
Ms Long said it was absolutely crucial security force data sharing continued.
She added the withdrawal agreement had an impact on a future security partnership and met the Home Secretary Priti Patel on September 10.
The minister raised what she said was lack of detail around negotiations and their implications for the Northern Ireland Protocol.