In a statement issued in Nairobi on Saturday, a copy of which was received by the News Agency of Nigeria, the Commission described the story as a concoction replete with falsehood.
It asked the public to refrain from interfacing with faceless groups or individuals who invest shamelessly in propagating irritants injurious to the cordial diplomatic relations between Nigeria and Kenya.
It also asked Nigerians in Kenya to go about their activities within the provisions of the laws of the host country.
The High Commission added that it remained resolute in executing its responsibilities and functions with every sense of professionalism and patriotism to Nigeria and to Nigerians.