A system and method are described, for use in cleaning of a vacuum chamber. The method comprising connecting a vacuum chamber to a plasma generating unit via a plasma connection port and connecting the vacuum chamber to a high vacuum pumping unit via a pumping port. A flow conductance through the plasma connection port to the vacuum chamber is controlled to limit passage of charged particles and cleaning substances produced in the plasma generating unit, to thereby maintain a working pressure inside the vacuum chamber while cleaning the vacuum chamber by said cleaning substances.