The union has backed the 37-year-old after he was accused of using inappropriate language, understood to have been of a racial nature, towards two Blues players.
The Premier League encounter became a heated affair after Clattenburg sent off two Chelsea players in quick succession while the game was still tightly poised at 2-2.
However, the Blues' complaints were not that the referee performed poorly, but that he used offensive language - allegedly later clarified as of a racial nature - towards Juan Mata and John Obi Mikel.
In light of the complaint, the referees' union has released a statement confirming it's commitment to fighting racism, but offering it's full support to the referee.
"Prospect is committed to helping to eradicate racism in football and in society generally," the statement read. "In the context of that commitment, Prospect is offering full support to Mark Clattenburg in relation to the allegations made against him.
"It is now important that the allegations are fully investigated through the proper process as quickly as possible. We will be making no further comment at this stage."
Clattenburg will now wait to hear whether the FA will launch an investigation into the allegations.
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