The 47-year-old Australian's legal action comes with speculation mounting that Ecuador is preparing to end its stand-off with the British government by terminating his high-profile stay.
Assange found refuge in the embassy in 2012 after a British judge ruled he should be extradited to Sweden to face allegations of sexual assault. That case has since been dropped but Assange fears being extradited to the United States to face charges over the WikiLeaks website's release of troves of sensitive US government files.
WikiLeaks said its general counsel arrived in Ecuador on Thursday to launch a legal case against the government for "violating [Assange's] fundamental rights and freedom".
"The move comes almost seven months after Ecuador threatened to remove his protection and summarily cut off his access to the outside world, including by refusing to allow journalists and human rights organisations to see him," WikiLeaks said.
"It is not a comfortable situation, it is an inhuman situation, because the solution that should already have been reached by the involved states is extending over time," said the lawyer. "We have to find a solution, to comply with what is established by the international law and certainly not aggravate the humanitarian situation of an individual, as I say, who is not deprived of liberty."
Britain's Press Association news agency said the case is expected to be heard in Ecuador next week.
US Attorney General Jeff Sessions said in March 2017 that arresting Assange for leaking sensitive US government files through his websites was a "priority."