The likelihood is that Hughes will bring in some experienced backroom staff should his appointment be confirmed.
Hughes, who was born in Wrexham, began his coaching career with Barry Town and then worked for Port Talbot Town, and also had a spell working for the Football Association of Wales.
Williams has left Newport having joined the club’s staff when Graham Coughlan was in charge in 2023, while Thomas arrived from Haverfordwest County last October.
Speaking about the two departures on the club website, Jenkins said: “It goes without saying that we thank both Daf and Rob for their efforts and commitment to the club during their time here.
“I am sure they will both be successful with their new challenges ahead and everyone at the club wishes them well for the future.”
Newport added that as well as “finalising” a new management team, they are working on a list of which players will be released and retained this summer.