A Coastguard spokeswoman said they were hoping to get in contact with the parents of the two boys.
She said: "We would like to hear from the parents to confirm that the children are, in fact, safe."
It is understood that the boys were reported missing at midday but the parents had not been in contact with the emergency services since about 1pm.
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Police said they were called to an incident at Hamerton Zoo in Cambridgeshire but gave no further details apart from no animals escaped.
A man's body has been discovered in the sea off the Kent coast.