This directive is seen as protective measure amid the worldwide outbreak of the novel coronavirus.
The church also urged Ministers and Extraordinary Ministers of Holy Communion to wash their hands or use sanitizer before and after the distribution of Holy Communion.
The document signed by the President of the Conference, Most Rev. Philip Naameh said: ”All are encouraged to receive Holy Communion in the hand. Ministers and Extraordinary Ministers of Holy Communion should wash their hands or use sanitizer before and after distributing Holy Communion. Avoid handshakes and embracing one another during Kiss of Peace.”
Last week, Nigeria confirmed the first coronavirus in sub-Saharan Africa.
The patient is an Italian citizen who works in Nigeria and flew into the commercial city of Lagos from Milan on 25 February.
Authorities say he is stable with no serious symptoms and is being treated at a hospital in the city.
Elsewhere on the continent, Algeria and Egypt have also confirmed cases of the disease.
The World Health Organization (WHO) had warned that Africa's "fragile health systems" meant the threat posed by the virus was "considerable".