Shettima had on Tuesday attacked UN organisations and over 120 non-governmental in the north-east, accusing them of underperforming and misusing funds meant for people displaced by the Boko Haram crisis.
He singled out UNICEF for rebuke, but also praised eight organisations for their efforts.
Last month, the UN launched a $1bn (£825,000) appeal for those facing hunger and starvation in the region.
Short of calling the group thieves, the governor said most of the NGOs were using funds released to them for servicing only their overheads and personnel costs.
He accused them of enriching selves in the name of providing service to victims of Boko Haram in his state and asked them to leave the restive region.
Reacting to the claims, Edward Kallon, UN Resident Humanitarian Coordinator to Nigeria, denied the accusations saying the agency had scaled up their presence and assistance in the area.
Alongside top officials of the United Nations system in Nigeria, he paid a visit to the Government House Maiduguri, Borno State, for a fence mending meeting with the Governor.
At the event, Kallon made a detailed presentation of the UN mission for the North-East and Borno in particular.
Appreciating their visit to the state, Shettima said the media misquoted him in the report.
He said he did not include UNICEF or any of the top UN organisations in the list of the NGOs he wanted out of Borno state.
In his speech, Kallon, implored Governor Shettima on the need to understand the dynamics of the politics surrounding humanitarian services.
He also asked the governor to be wary of the media, which he said could stall efforts being made to channel more funding and supports for the victims of Boko Haram.
He urged Governor Shettima to always consult them, being experts in the humanitarian business, anytime he has questions or observed something he is not pleased with.
Governor Shettima said he was “very sorry” for the embarrassment his statement about nonperforming NGOs might have caused the UN system.
He said Borno government and the UN must always speak with one voice, as having contrasting views on the same issue might scare donors away.
Kallon said, “One thing you have to know about the humanitarian business is that it is a big, big politics. UN are now stabilising their staffs here by bringing in their permanent staff; they are trying to bring their staff from Syria and other places – people who have the experience in dealing with the humanitarian business.”
According to him, UN agencies have currently reached over 2 million people with humanitarian assistance as against barely 100,000 people as at October 2016.
The UNDP Chief therefore advised the Federal Government and relevant authorities at all levels no to politicise the role and response of the UN and international communities in the North-East.
Shettima said he was impressed with the vision the UN has for Borno state and as such his government will be disposed to working with them.
In the past, the Governor said the state never received any cash donation from international donors for IDPs in the last four years.
The UN said that nearly 5.1 million people in three north-eastern states were expected to face serious food shortages as for a third year in a row farmers had been unable to plant, fearing unexploded improvised devices left behind by militants.
Urgent aid was needed for some 100,000 people, mostly children, at risk of dying of starvation.
Nigerian military forces backed by troops from Niger, Cameroon and Lake Chad have, in the past few months, pushed Boko Haram out of areas they previously controlled,
revealing thousands of people living in famine-like conditions.
The conflict, which has killed more than 15,000 people and uprooted 2.4 million has also pushed food insecurity and malnutrition to emergency levels in northeast Nigeria. (TV360 Nigeria)
