He said his decision was based on advice from senior doctors who have made it clear that Caldwell, who was hospitalised overnight, faces a medical emergency.
Charlotte Caldwell, of Castlederg in Co Tyrone, Northern Ireland, said the youngster was showing signs of improvement after receiving three doses of the drug at Chelsea and Westminster Hospital.
Billy's mother says she wants to discuss Billy's future with MPs on Monday: "I want to meet the Home Secretary and Health Secretary (Jeremy Hunt), urgently, this week, to get assurance that not only will Billy's meds never again be removed, but to call for an urgent review of the overall policy on medical cannabis as it affects everyone who could benefit".
When Billy and his mother returned to the United Kingdom from Canada with the supply for his treatment this week, the cannabis was taken into customs possession at Heathrow Airport.
She said her son suffered two severe seizures overnight, and that the cannabis oil is the only substance that can prevent life-threatening seizures for Billy.
Ms Caldwell credits the oil with keeping the boy's seizures at bay, saying he was seizure-free for more than 300 days while using it.
The Home Office, or interior ministry, could not immediately be reached for comment about Billy's hospitalisation.
"My experience throughout this leaves me in no doubt the Home Office can no longer play a role, in fact play any role, in the administration of medication for sick children in our country".
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She was returning with Billy, 12, from Toronto's Hospital for Sick Children, where doctors had placed him on a clinical trial of the medication.
Keen to get back to her son's bedside, she said: "I am full of hope - this is my little boy's anti-epilepsy medication".
She said her son was too ill to travel to Canada to get his medication.
She criticised outdated laws and called for "more humane policies" while vowing to fight for others in the United Kingdom to have access to the medication they need.
A Home Office spokesperson said: "We are deeply sympathetic to the extremely hard situation that Billy and his family are in".
But, she added, the Home Office had been working with the family "extremely hard" throughout the night to negotiate access to the medication.
Billy started the treatment in 2016 in the U.S., where medical marijuana is legal.
Billy, 12, from Castlederg in Co Tyrone, has a form of epilepsy meaning he can not get help through medication or diet.
Billy became the first person in the United Kingdom to receive a prescription after his local GP in Northern Ireland, Brendan O'Hare, began writing scripts. O'Hare was summoned to a meeting with Home Office officials recently and told to stop.