Mr Assange has been holed up in the building since 2012, when he was formally given asylum by the Ecuadorian government.
The UK has been trying to extradite Mr Assange to Sweden, where authorities have been seeking to interview him in relation to four allegations of sexual assault.
The investigation into three of the four allegations was dropped today because the time limit to interview Mr Assange had expired. He is still wanted for an accusation of rape.
Britain’s ambassador in Quito will make a formal protest about Ecuador’s actions today, the Foreign Office has said.
“Ecuador must recognise that its decision to harbour Mr Assange more than three years ago has prevented the proper course of justice,” FCO minister Hugo Swire said.
“It is completely unacceptable that the British taxpayer has had to foot the bill for this abuse of diplomatic relations. I want to make clear that as an allegation of rape remains outstanding, the UK continues to have a legal obligation to extradite Mr Assange to Sweden.
“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. I will also repeat this to the Ecuadorean ambassador in London.”
In February, it emerged that the Metropolitan Police had so far spent approximately £10m on guarding the embassy since Mr Assange's flight.