On Monday, Prime Minister Boris Johnson announced that gatherings of more than two people are now banned as part of the government's efforts to halt the spread of COVID-19, the disease caused by the coronavirus.
The new rules allow only four reasons for leaving the house: shopping for basic necessities like food and medicine, one form of daily exercise, for medical needs and commuting to work that cannot be done from home.
In a message to the nation from Downing Street, the prime minister advised that any contact involving two people not living in the same home should be carried out while keeping at least two metres (6.5ft) apart.
Speaking at the government's daily coronavirus news conference on Tuesday, England's deputy chief medical officer Dr Jenny Harries said these rules would also apply to non-cohabiting partners.
She warned they could pass on the virus if they continue to visit each other at their respective homes.
Dr Harries said couples could "test" their relationship and move in together while the lockdown restrictions are in place.
"If you are two individuals, two halves of the couple, living in separate households then ideally they should stay in those households," she said.
"The alternative might be that, for quite a significant period going forward, they should test the strength of their relationship and decide whether they should permanently be resident in another household."
Dr Harries said that couples in such a situation should make a decision and stick with it, otherwise they could be putting their families in danger.
"What we do not want is people switching in and out of households," she added.
"It defeats the purpose of the reductions in social interactions and will allow the transmission of disease."
Mr Johnson's official spokesman earlier told reporters that "common sense" should be used by partners living apart.
Asked about the dilemma facing such couples, the spokesman said the "rules are clear".
"I think you should look at those rules, they are an instruction given by the government for a specific reason which is to save lives," they said.
"People should follow the rules and do so in a common sense way."
He added: "When you are out of the house, you should only do so with members of your own household or if it is for work reasons."
The exemptions to the rules on being outside apply in two scenarios - key workers taking their children to school and children living with two separated parents, the spokesman said.
Earlier, Cabinet Office minister Michael Gove had to backtrack after initially saying the children of separated parents should not move between households.
But Mr Johnson's spokesman said: "Two particular issues have been raised which are clear in our guidance.
"Those are around key workers taking their children to school and also the issue of separated parents and ensuring children can move between those two carers."