(Adds statement from Ecuadorean government)
LONDON, Aug 13 (Reuters) - Britain said on Thursday it would make a formal protest to Ecuador over its decision to provide asylum to WikiLeaks founder Julian Assange in its London embassy and so prevent his extradition to Sweden over alleged sex crimes.
"Ecuador must recognise that its decision to harbour Mr Assange more than three years ago has prevented the proper course of justice," British Foreign Office minister Hugo Swire said in a statement.
The comments came after Swedish prosecutors dropped inquiries into three allegations of sexual molestation and unlawful coercion against the 44-year-old Australian as they had run out of time to bring charges.
However, they said they would push on with an investigation into an allegation of rape made in 2010 against him.
Assange, who denies any wrongdoing, has been holed up in Ecuador's London embassy since June 2012 to avoid being extradited to Sweden.
He fears he would then be extradited to the United States where he could be tried for one of the largest information leaks in U.S. history after publishing thousands of secret U.S. diplomatic cables five years ago which infuriated Washington.
Assange breached his bail conditions to go to the embassy and British police have guarded the building in the upmarket central London neighbourhood of Knightsbridge day and night ever since, at an estimated cost of more than 10 million pounds ($15.6 million).
"It is completely unacceptable that the British taxpayer has had to foot the bill for this abuse of diplomatic relations," said Swire, adding Britain still had a legal obligation to extradite Assange while the rape allegation remained outstanding.
"I have instructed our ambassador in Quito to reiterate to Ecuador that the continuing failure to expedite the Swedish Prosecutor's interview and to bring this situation to an end, is being seen as a growing stain on the country's reputation."
In a statement, Ecuador's Foreign Ministry said it was saddened that Assange's confinement had lasted three years, adding that its government had offered "31 times" to facilitate "open judicial process" in Sweden.
Ecuador's government "deplores the continued inaction of British and Swedish authorities over almost 1,000 days," read the statement. ($1 = 0.6421 pounds) (Reporting by Michael Holden; Additional reporting by Alexandra Valencia in Quito and Girish Gupta in Caracas; Editing by Kate Holton, Gareth Jones and Bill Rigby)