UNITED NATIONS (Reuters) - The United Nations envoy to Somalia warned on Thursday that the arrest of a former militant leader could deter others from choosing politics over violence, speaking publicly about the incident despite being kicked out of the country just days earlier for privately expressing his concerns to the government.

FILE PHOTO: Nicholas Haysom, the then head of the U.N. Assistance Mission in Afghanistan, listens to a question during a news conference in Kabul, Afghanistan February 14, 2016. REUTERS/Mohammad Ismail

Nicholas Haysom briefed the U.N. Security Council in New York but did not address a statement issued by Somalia’s foreign affairs ministry late on Tuesday that accused him of interfering in internal affairs and said he “cannot work in this country.”

Haysom had raised questions in a letter on Sunday about the involvement of U.N.-supported Somali security forces in the arrest of a former militant of the Islamist al Shabaab group who was blocked from running in a recent regional election.

He told the 15-member Security Council that the allegations of interference by the federal government in the regional election and the violence that followed the former militant’s arrest “does not bode well for the upcoming electoral processes in other regions or for the 2020 national elections.”

“This may also have implications for the likelihood of future al Shabaab defectors who may be considering exchanging violence for a political path,” said Haysom, a South African.

Somalia showed no signs on Thursday of backing down from its decision to effectively make Haysom persona non grata. The United Nations said on Wednesday it was looking into the matter and that Haysom would meet with U.N. Secretary-General Antonio Guterres on Thursday.

The United Nations is a major backer of Somalia, a country that has lacked strong central government since 1991. The government’s decision on Haysom could intensify a confrontation between Mogadishu and the semiautonomous regions.

Somalia’s U.N. Ambassador Abukar Dahir Osman told the Security Council on Thursday that the Somali people wanted “Somalia leading international support, not international support leading Somalia.”

“Somalia distinguishes between the institutions that we are part of and individual conduct that’s had detrimental effect on our fragile nation,” he said. “We reject the criticism and attempt to re-brand renewed terrorists as an ice cream salesperson without redeeming themselves.”

Al Shabaab has sought for over a decade to topple the central government and implement its strict version of Islamic law. It was driven out of the capital in 2011 but maintains a foothold in some regions.