The decision is almost four weeks behind England, where farmers and owners of birds have had to keep them inside since November 7.
NFU Cymru has welcomed the news.
The farmers' union recently wrote to the Welsh Government requesting that mandatory housing measures be introduced "urgently".
In addition to the mandatory housing of birds, keepers must also complete and act upon a bespoke biosecurity review of the premises where birds are kept. This is to minimise the risk of the virus entering bird houses.
These new measures are in addition to the stringent biosecurity measures already in place under the Wales Avian Influenza Prevention Zone.
NFU Cymru Poultry Board chairman Richard Williams said: “Following the NFU Cymru Poultry Conference on November, 21, NFU Cymru wrote to the Minister for Rural Affairs to ask that Welsh Government urgently introduce mandatory housing measures to help reduce the risk of the virus causing further devastation to our poultry flocks.
"I am pleased that the Welsh Government has listened to our concerns and our sincere hope is that these housing measures, alongside the existing and additional biosecurity requirements that we are undertaking, will help minimise the impact of avian influenza on the Welsh poultry sector.
“These measures apply to all poultry keepers, whether you have one hen in the garden or a large poultry business, and I urge everyone to remain vigilant.
“This is a really challenging time for the Welsh poultry sector, but producers are doing all they can to protect their birds and to maintain production of healthy, nutritious and affordable poultry meat and eggs for our consumers to enjoy.”