Gardaí yesterday confirmed the memorial, which is at the spot where 11-year-old's body was found in Inch, Co Cork, was vandalised.
A senior garda spokesman said Robert's family was devastated by the news.
Gardaí searched the area yesterday after getting a tip-off from a member of the public. They are satisfied the attack was deliberate. However, they are not aware of any motive.
They found a metal cross put up by the landowner was missing along with pictures of Robert and some of his toys.
"We discovered some of the toys thrown into the nearby valley and others items scattered around the general area," the garda spokesman said.
He described the vandalism as "a particularly vile and despicable act" and added that they had evidence the shrine was intact on Tuesday afternoon.
They believe it was attacked between Tuesday night and yesterday morning. Last night most of the shrine had been restored.
Robert disappeared from his home in Midleton on January 4, 2005. Following intensive searches his body was discovered, eight days later and nine miles away, at Inch Strand. The discovery was made possible using mobile phone triangulation techniques.
Gardaí closed the remote site for four days while they carried out a detailed technical examination. When it was reopened to the public on January 16, 2005, the shrine was erected by family members and friends. Dozens of flowers were also left at the scene by strangers shocked by the killing.
A garda spokesman said: "Nothing has ever happened to this shrine before. We are very anxious to contact anybody who was in the area of Inch Strand between Tuesday night and Thursday morning and who may have seen anything suspicious."
He said anybody with information should contact Midleton garda station at (021) 4621550.
Robert's next door neighbour, Wayne O'Donoghue, pleaded guilty last January to his manslaughter.
He given a four-year sentence at a special sitting of the Central Criminal Court in Ennis.
However, on February 20 the Director of Public Prosecutions lodged an appeal against the leniency of sentence.
It is understood the DPP laid out six separate grounds for the appeal.