He was President Michel Martelly's third nomination when appointed in October, ending a long stalemate. For several weeks there have been reports of power struggles that prompted the UN to intervene.
On Thursday Mariano Fernandez, the special representative of the UN secretary general in Haiti, said there were "repeated crises" between the parliament, president and prime minister.
"[These] undermine the proper functioning of the institutions and the democratic process," he said.
So far President Martelly has not announced any replacement or caretaker prime minister.
One of the issues causing division was a parliamentary commission investigating the nationality of government ministers.
Many officials in Haiti and elsewhere in the Caribbean spend considerable time overseas.
The commission is investigating whether some senior administration officials have dual citizenship, which is prohibited under the constitution.
Mr. Conille originally trained as a doctor and had previously worked with the UN.
He was an aide to former US President Bill Clinton when he was a UN envoy to Haiti.
When Mr Conille took office he pledged to create thousands of jobs by attracting foreign investment to help rebuild the country.
BBC Latin America & Caribbean