Ms Caldwell said her son's seizures, each of which is potentially fatal, had returned on Tuesday after the medication was seized.
A family spokesman said the medication was on its way to London's Chelsea and Westminster Hospital early yesterday afternoon.
Norman Baker, a former Home Office minister and Lib Dem MP, said he had called for a change in the laws on medicinal cannabis when in office but had been "obstructed all the way" by then home secretary Theresa May, who he accused of having "some sort of pathological fear of cannabis".
On Friday night the Home Office said it was in contact with Billy's medical team and would "carefully consider what options are available" if they advise a particular type of treatment is urgently required.
The Home Office previously said it sympathised with Caldwell's situation but it had a duty to stop banned substances from entering the country. He said his decision was based on advice from senior doctors who say that Caldwell, who was hospitalized overnight in London, faces a medical emergency.
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Doctors said it was too risky to treat him with "rescue meds" at home and he can now be treated only with hospital-administered medicine.
Charlotte Caldwell had arrived in Heathrow yesterday morning and declared to customs that she was in possession of cannabis oil.
The 12-year-old boy is now too ill to travel back to Canada for treatment, meaning the only effective medication is locked in secure storage in the Home Office in London.
She says the cannabis oil, which is banned in Britain, is the only substance that can prevent life-threatening seizures suffered by her son.
The child, from Castlederg in Co Tyrone, started the treatment in 2016 in the USA, where medical marijuana is legal.
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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.
However in May, the Home Office told his GP to stop the prescription.
The mother of a boy with severe epilepsy has called for a meeting with the home secretary and health secretary to talk about making medical cannabis legal for children who have similar conditions to her son.
Charlotte criticised the "dreadful, horrific, cruel experience" that has deeply affected 12-year-old Billy, saying: "His little body has been completely broken and his little mind".
"Billy is in the care of medical professionals who are best placed to assess the care and treatment that he requires".
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"I truly believe that somewhere in the Home Office there's someone with a heart and I truly believe that Billy was pulling on their heart strings", she said.