The increasingly farcical situation leaves the disgraced singer in international limbo.
He has already been barred from entering Thailand after travelling there when he was released from a Vietnamese prison.
A Foreign Office spokesman said the 64-year-old, travelling under his real name Paul Gadd, was denied entry to Hong Kong and had now returned to Bangkok.
The Foreign Office spokesman said: "We have been informed by the Hong Kong authorities that Mr Gadd was denied entry to Hong Kong and has returned to Bangkok.
"Mr Gadd was in contact with us seeking consular assistance."
The spokesman did not seek what form of assistance Glitter sought.
He was refused entry to the Chinese territory last night after flying there on Thai Airways service TF 602, the Foreign Office confirmed.
Chinese authorities informed their UK counterparts that they had barred Glitter from the country after his arrival at 11pm local time (1600 BST).
Immigration police at Hong Kong airport said privacy laws meant they could not comment on Glitter's case.
Glitter spent more than 20 hours in the transit lounge at Bangkok airport yesterday following his release from a Vietnamese prison on Tuesday.
He had served two years and nine months of a three-year sentence for abusing two girls aged 10 and 11.
Under the terms of his release he was due to board a connecting flight to London's Heathrow airport but refused claiming ill health.
He was barred entry into Thailand and immigration officials said Glitter would be taken to a detention centre if he continued to refuse to leave the country.
Lieutenant General Chatchawal Suksomchit, the chief of Thailand's immigration police, said Glitter was denied entry because under Thai immigration laws those convicted of child sex abuse in a foreign country could be barred.
Yesterday afternoon Thai Airways and Thai Police confirmed that he had boarded a flight to Hong Kong.
While on board the flight Glitter tried to arrange a VIP welcome at Hong Kong airport, the Daily Mail reported.
Calling from the plane he spoke to ground staff, saying: "I am quite famous and hard of hearing. Please can you arrange for an escort for me at the other end?" the newspaper reported.
When asked why he was making the trip, Glitter reportedly said: "I am travelling to Hong Kong for medical treatment."
Yesterday Home Secretary Jacqui Smith said Britain could not enforce Glitter's return but must have a plan if he did.
If and when he arrives in the UK, he will be met at the airport by police officers and served with an order which effectively will put him on the sex offenders' register.
Asked about Glitter while on a visit to special constables in Tooting, south London, Ms Smith said: "What I am concerned about is, whoever the individual sex offender is, that we have in place the necessary provisions to monitor them."
Ms Smith yesterday announced tighter controls on the movement of paedophiles but she dismissed a suggestion that the Government had wanted a "celebrity paedophile" to promote the crackdown and had found it "embarrassing" that Glitter had not come home.
"No paedophile is a celebrity, every paedophile needs to be controlled," she said.
She told GMTV Glitter was "despicable" and said it was "pretty hard to imagine it would be legitimate for him to travel abroad again".
The announcement included increasing the length of foreign travel orders preventing convicted paedophiles from going abroad, from six months to up to five years.
Glitter was treated for a heart condition while in prison and he has said he wants to return to the UK for treatment.
Asked if she was comfortable with Glitter using the NHS and taking up police time, Ms Smith told GMTV: "I think it's right that we use police time to monitor sex offenders.
"If you are a British citizen, you have the right to use the NHS, whatever we think about an individual, and this is a pretty despicable person."
Glitter was convicted of downloading child pornography in the UK in 1999 after a computer repair shop found the images on his laptop and he served two months of a four-month sentence.
He left the country and moved to Spain and Cuba before travelling to south-east Asia where he escaped detection until he was tracked down by reporters.
He was kicked out of Cambodia after facing allegations of sex crimes and moved to the Vietnamese coastal resort of Vung Tau.
The two girls at first made allegations of rape, which carries a death sentence, but were reportedly paid off with £1,175.
Glitter was arrested trying to leave the country and stood trial, pleading not guilty and claiming he was teaching the girls English. He was convicted and sentenced to three years in March 2006.
Dr Zoe Hilton, policy advisor at the NSPCC, said: "This clearly illustrates why it's so important to have binding agreements between countries which will prevent sex offenders hopping from one place to another and possibly going underground where they will pose a serious threat to children.
"Offenders like Glitter can and should be chaperoned while being deported back to the UK where they can be properly monitored. It is disappointing this latest development was not anticipated and proper arrangements put in place to make this work.
"This case is important because it highlights how easy it is for UK offenders to move around freely when they are overseas - even those who pose a high risk to children."
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