A retail group says the removal of 'click and collect' options for shops takes away "a lifeline for SMEs".
Non-essential shops have been instructed to end the services immediately, and are only be permitted to operate delivery services moving forward.
However existing orders can be fulfilled.
Schools will also remain closed at least until the end of the month, as part of new public health restrictions.
Jean McCabe is deputy chair of Retail Excellence and owner of Willow.ie.
She told Newstalk Breakfast they hope to be the first to re-open when coronavirus numbers fall.
"It is obviously a setback for retail - retail has proven to be a really safe environment, and the Government have said that themselves.
"But the overarching objective here is to reduce people's movements".
"As it is a setback, it's also understandable - the reasoning behind it - and we just hope that as we get the virus under control that the retail industry will be recognised for being the safe environment that it is".
She said she is hopeful non-essential stores, and facilities like 'click and collect', will return as soon as possible.
"Click and collect would have been a lifeline for SMEs throughout the lockdown.
"I mean stores that weren't necessarily already trading online that were able to facilitate orders through phone calls [or] through their social media channels, it's them that are really going to suffer at the moment with the removal of the click and collect."
'80,000 workers laid off'
Announcing the new measures on Wednesday, Taoiseach Micheál Martin said the decisions we all make in the coming month will "directly affect" how many people get sick and how many die.
“As I stand here, hospitals across the country, across these islands and across Europe are under siege from the disease with already exhausted healthcare workers now facing a tsunami of infection even greater than the first wave,” he said.
Meanwhile, non-essential construction sites will close at the end of the week, with exceptions for ‘essential’ projects including those related to housing and health.
Tom Parlon, the director-general of the Construction Industry Federation (CIF), said some 80,000 workers will be laid off at the end of this week.
"We do appreciate that the whole COVID situation has deteriorated very substantially and is very, very worrying".
"We're going to be about expediting our return to work and working on that".
He said "quite a substantial amount of projects" will still be operating through the lockdown.
But that "up to 80,000 workers will be laid off from Friday evening" and go on to the Pandemic Unemployment Payment (PUP) scheme.