BBC royal correspondent Nicholas Witchell said Her Majesty had been in touch with the Prince of Wales and the Duke of Cambridge on Thursday.
They directed senior staff to work with the Sussex household and government.
It comes as the Royal Family was said to be "hurt" at the couple's statement.
Prince Harry and Meghan did not consult any other royal about making their personal statement, palace sources have told BBC royal correspondent Jonny Dymond.
In their announcement on Wednesday evening, Prince Harry and Meghan revealed they intend "to step back as 'senior' members of the Royal Family, and work to become financially independent".
They plan to split their time between the UK and North America, while "continuing to honour our duty to the Queen, the Commonwealth, and our patronages".
The decision came "after many months of reflection and internal discussions", they added.
Buckingham Palace was "blindsided" by the couple's statement, said our correspondent Jonny Dymond.
There had been talks within the Royal Family about the Sussexes' future - but they were at an early stage, he said.
In a statement on Wednesday, Buckingham Palace said: "We understand their desire to take a different approach, but these are complicated issues that will take time to work through."
Despite the couple's decision, Harry will remain sixth in line to the throne.
Last October, Prince Harry and Meghan publicly revealed their struggles under the media spotlight.
Over Christmas, the couple took a six-week break from royal duties to spend some time in Canada with their son, Archie, who was born in May.
After returning to the UK on Tuesday, Harry, 35, and Meghan, 38, visited Canada's High Commission in London to thank the country for hosting them and said the warmth and hospitality they received was "unbelievable".
Former actress Meghan, who is American, lived and worked in Toronto during her time starring in the popular US drama Suits, and she has several Canadian friends.