Parents of young children have said they fear losing out financially by following the "stay at home" message.
Some are concerned they will no longer be eligible for government childcare funding if they choose to keep children home, and could lose their place if they do not pay for it themselves.
Nurseries and other childcare providers can stay open under lockdown rules.
The Welsh Government said it would continue to fund childcare places, if it was a "valid" Covid-related absence.
But one mother told BBC Wales that parents should not be "penalised financially" for keeping young children at home during lockdown.
Gemma, a 36-year-old lawyer, decided to withdraw her child from nursery temporarily while the rest of the family were at home.
When she informed the nursery, she was told that funding through the Childcare Offer for Wales had been withdrawn for children who did not return after the Christmas break.
She said she had been left with two options.
"Either send my son to nursery in a national lockdown - in complete contradiction to the clear message to stay at home, to avoid all but essential travel and avoid mixing with others - in order to maintain the funding he is eligible for.
"Or lose funding entirely and pay the full price... to retain his space until he returns to nursery."
She does not want to risk losing her son's usual childcare arrangements because it would cause further disruption to him and her ability to work.
She added: "It is surely a reasonable expectation that parents should be provided with the choice to temporarily keep their children at home, in lockdown, without being penalised financially for doing so."
What is the Childcare Offer?
The Childcare Offer allows working parents of children aged three or four to claim for up to 30 hours of early education and childcare a week.
Parents claim through their local authorities who, in-turn, pay the fees for the hours covered by the Welsh Government scheme.
Jane May, from Cupcakes Childminding in Flintshire, said if childcare providers did not get funding they would have to terminate the contract and try to fill that place.
She mainly looks after the children of keyworkers, but said other childminders have been forced to close during the pandemic.
"We're trying to stay afloat so we can offer that childcare when the families are ready to send their child again," said Ms May.
"It's not easy to switch childcare. You have to trust someone to look after your young children, and the child is uprooted. They have been through enough in this pandemic."
Whether and when funding would restart for parents keeping their children at home would be up to each local authority - and Welsh Government said councils "will look at individual circumstances".
Purnima Tanuku, chief executive of the National Day Nurseries Association, said the sector in Wales had faced immense pressures under the pandemic.
"We continue to urge the Welsh Government to do everything it can to ensure nurseries and early years settings are supported so they can continue to provide places for children in the future, even if they aren't able to attend now," she said.
The Welsh Government said local authorities could carry on paying the fees where there is a "valid Covid-19 related reason" for a child's absence - including a member of the household self-isolating.
"If the non-attendance continues beyond a four-week period which aligns with most childcare providers' notice period for private customers, the local authority may decide to extend the funding for a short period but that decision will depend on the specific circumstance of the family," said an official.