Police had detained the 39-year-old man in a hotel in Waltham Forest on 5 October after reports a teenage boy had been attacked.
The suspect was taken into custody and questioned before being bailed to return on a date in early January.
The suggestion the man had gone missing was revealed by Tory MP Greg Smith during a Commons debate on Wednesday.
Mr Smith told the Commons: “Buckinghamshire Council learned third-hand from a London borough just this morning that an asylum seeker who is under investigation for a very serious offence was transferred to the asylum hotel in Buckingham.
“He was not escorted into the premises and has since gone missing.”
He continued: “That process is wholly unacceptable,” the Buckingham MP said, while asking for a commitment “that everything possible is being done to apprehend that individual and ensure that until that investigation is completed they are in secured accommodation.”
Home office minister Robert Jenrick replied: “That does sound like a very concerning incident and he has my assurance that I will raise that with the Home Office and indeed with the police and will report back to him.”
A child, under the age of 13, was also allegedly sexually assaulted at the same site in Waltham Forest.
A Home Office source said: “The bail conditions of this suspect are a matter for the police and we do not have any powers to detain him. There is no evidence he has absconded.”
Following the alleged attacks, Grace Williams, leader of Waltham Forest Council, wrote to Suella Braverman, the home secretary, to express “major concerns” at the “lack of safeguarding” at the hotel.