Speaking to ITV’s GMB programme, the Cabinet Office minister said children should “stay in the household they are currently in”.
“We should not have children moving between households,” he said when questioned about what parents who do not live together should do.
Gove added: “I know this is incredibly difficult, this is a time of – an emotionally fraught time and a difficult one.
“Wherever possible, if there can be contact through social media or non-physical contact then that should carry on.”
But the senior minister quickly moved to clarify his comments, which were at odds with the official government guidance.
Gove also later told BBC Radio 4′s Today programme: “One of the things that is clear, if it is the case, that children under the age of 18 need to move from one parent’s home to another parent’s home, that is allowed.”
Boris Johnson last night ordered people only to leave their homes under a list of “very limited purposes”.
The prime minister also dramatically banned public gatherings of more than two people and ordered the closure of non-essential shops.
In an address to the nation from Downing Street, Johnson ordered people only to leave their homes to shop for basic necessities “as infrequently as possible”, and to only perform one form of exercise a day.
They can also seek medical help, provide care to a vulnerable person or travel to work if “absolutely necessary”, under the measures to last until at least Easter Monday.
“That’s all – these are the only reasons you should leave your home,” he said.
“You should not be meeting friends. If your friends ask you to meet, you should say no. You should not be meeting family members who do not live in your home.”
A failure to follow the rules could see police dispersing gatherings and imposing fines, which government officials said would start at £30.
After the UK death toll hit 335, the PM ordered the immediate closure of non-essential stores including those selling electronics and clothing.