Speaking after a consultative meeting in Kitale, Mbaruku said the resettlement of more refugees at Kakuma camps has been halted due to a lack of infrastructure.
The meeting had been convened following an influx of asylum seekers to Kitale Transit centre and a humanitarian crisis at the facility.
At-least 8,000 asylum seekers have been received at the transit center since January this year.
While hundreds of the affected families have been transported for settlement at Kakuma, about 1,600 others are stranded at the transit center where they are facing humanitarian challenges.
So far, two deaths linked to starvation have been reported at the facility.
Mbaruku who led teams from UNHCR, Kenya Red Cross, and the County government of Trans Nzoia to assess the humanitarian situation of the refugees said the families will continue living at the facility until their resettlement issue is conclusively handled.
Mbaruku disclosed that the majority of families at the transit center are onward movers.
He revealed ongoing talks between Kenya and Uganda governments on the inflow of refugees from the resettlement camps in Eastern Uganda.
"Kenya wants to understand why this movement of refugees from Uganda and possible intervention to stop the inflow," said Mbaruku.
The meeting was attended by UNHCR representative to Kenya Ms Carolyne Van Buren, Trans Nzoia County Commissioner Gideon Oyagi, Trans Nzoia County Executive Member for public service Sammy Ojwang and Ronald Masindano and Micheal Ayabei from Kenya Red Cross Society.
Mbaruku lauded the host County government for providing free medical services to the refugees.
The county government has provided a mobile clinic at Kitale ASK Showground where the families are temporarily sheltered.
Ms Van said the UN agency would continue to work with the Kenya government to address and support the concerns of the refugees.
Mbaruku asked the refugees and host communities to adhere to Refugee Act 2021.
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The Act stipulates that the refugee be confirmed in designated areas.