The crucifix was actually removed because of classroom refurbishment, and it will be reinstated once the work is completed, the Foundation for Educational Services said.
It expressed its support for the Child Support Worker who had 'nothing to do' with the matter.
The case was allegedly first reported by a parent and raised a storm in a section of the social media, with vitriolic comments and demands for an official explanation for the 'unacceptable' development.
MUT demands action
The Malta Union of Teachers also leapt to the classroom assistant's defence, saying on Friday morning that it expected authorities to take action against the parent who spread the false rumour.
"This parent was out to taint the classroom assistant's name, insult her religious beliefs and show educators in a bad light," the union said.
"The MUT will not tolerate such irresponsible behaviour and urges authorities to take the necessary action to ensure that those who damage the educating profession pay the price," it added.