Occupy Justice activists found the makeshift memorial to Daphne Caruana Galizia "trashed" at the end of Carnival celebrations in Valletta.
Occupy Justice's Martina Farrugia said all plants around the memorial to the murdered journalist had been trampled on, the posters ripped down and candles overturned.
"This wasn't an accident," she wrote in a Facebook post that was also shared by Caruana Galizia's son Matthew.
"No, this was an act of cruelty. An act of aggression, harassment and disrespect aimed against the memory of a woman who was assassinated in her home country seven years ago."
The Great Siege monument opposite the law courts in the capital has hosted a memorial to Caruana Galizia since her assassination in 2017.
In the following years, the memorial was cleared several times by government employees acting on the orders of then-Justice Minister Owen Bonnici, until a constitutional court ruled that those orders breached protesters' rights.
In a 2021 interview with Times of Malta, Bonnici apologised for having "hurt people" with those orders.
Last year, however, PN said new photos of Caruana Galizia, along with candles that were laid on the memorial after the Victory Day commemoration were removed by the authorities.
On Wednesday, Farrugia said Occupy Justice activists cleared the rubbish, broken plants, cracked pots and papers and replanted the area.
"We wiped down the posters that had been muddied and stepped on and set them up again. Why? Because this national monument that Malta's citizens are so protective of deserves respect and care.
"Ironically, the people who destroyed the memorial were also disgracing the monument they proclaim to love so much."
Farrugia said the activists refurbished the Caruana Galizia memorial as it was protected by law and it was a call for justice to be served for the assassination of a journalist.
"We did it because even though seven years have passed, the hatred so carefully engineered against Caruana Galizia remains rampant in this country and, to me, it is unacceptable, after all their suffering and their monumental loss, for Daphne's family to come into Valletta and see this memorial trashed."
She urged prime minister Robert Abela to ensure the memorial was not only not cleared by government's employees but was also not be vandalised by the public.
"At a time when the world's order seems to be upside down, we need leaders to step up and lead, with integrity, with kindness, with respect and with enough awareness that this behaviour is rotten and needs to be nipped in the bud.
"Because despite appearances, this isn't the jungle, and might isn't right," she added.