Lisbon has expressed "regret" after admitting that it made a mistake when they passed on information about a pro-Navalny protest to Russia's embassy.
Lisbon City Council (CML) said the details referred to organisers of a January demonstration calling for Navalny's release from prison.
The city hall has to collect data from at least three people before authorising a protest.
"As required by law, the details of the three organisers were received," the council said in a statement.
"This information was forwarded ... to the entity/place where the demonstration was held, in this case, the Russian embassy," they added.
Lisbon said they had received a complaint after sharing this data and the details of the organisers had since been deleted.
"CML regrets that the reproduction of procedures instituted for situations of normal democratic functioning has not proved adequate in this context," the council said.
"Aware of this reality, the procedures were immediately changed to better protect the right to demonstrate and to freedom of expression."
But the council denied allegations that it had colluded with Russia when sharing the details of the activists, two of whom had Portuguese nationality.
"CML vehemently rejects any accusations and insinuations of complicity with the Russian regime," the statement read.
"CML has homogeneously complied with Portuguese Law, applying the same procedures to all types of demonstrations, regardless of the promoter and the addressee."
Lisbon confirmed that their internal procedures had been changed and it had not shared any information of activists who have since organised protests in front of the embassies of Israel, Cuba, or Angola.
"I was given a ridiculous explanation"
One of the activists, Ksenia Ashrafullina, who has lived in Portugal for eight years told Euronews she was now afraid of visiting Russia.
"I understand that my email was forwarded to two different email addresses," said Ashrafullina.
"I found it very strange, one was to the Russian embassy in Lisbon and the other to the Russian foreign ministry."
"I was given a ridiculous explanation," Ashrafullina added, saying that her name, address and telephone details had been shared.
The mayor of Lisbon has also issued a public apology for the incident, which he describes as a "regrettable mistake".
"Personal details should never have been handed to the Russian embassy," Fernando Medina told reporters.
Portugal's President Marcelo Rebelo de Sousa has also weighed in on the scandal and has reiterated that local administrations in Portugal cannot violate the fundamental privacy rights of citizens.
Supporters of Navalny in Russia have vowed to continue demonstrating, despite Russia banning the group for extremism on Wednesday.