In Athens they defaced the building and tore down images of embattled strongman Muammar Gaddafi, TV footage showed.
Private Mega channel broadcast footage of a few protesters inside the embassy compound in the affluent district of Psychiko, surrounded by debris.
One man was seen defacing the embassy entrance with graffiti while another tore off the plaque in front of the building.
The station said the protesters had piled up official portraits of Gaddafi and had torn up copies of the 'Green Book', the short text of the Libyan leader's political philosophy.
They also unfurled the Libya independence banner, the flag originally used by the country before Gaddafi's rise to power in 1969.
There were no reports of injuries in the incident.
Greek media reported that the Libyan ambassador was not present.
A police source said embassy staff had opened the gates to about 25 protesters and had not requested assistance from Greek authorities.
Gaddafi in hiding
Heavy fighting was raging in many parts of Tripoli on Monday, including Gaddafi's compound, after rebels swept through large swathes of the capital during the night.
The whereabouts of Gaddafi himself were unknown on Monday but one of his sons, Saif al-Islam had been arrested while another, Mohamed Gaddafi was interviewed by Al-Jazeera television cowering in his house, afraid to leave.
Meanwhile AP reported that police have surrounded the Libyan embassy in Sarajevo after Libyan nationals entered the building, threw Gaddafi's pictures out of the windows and raised the rebels' tricolour flag.
Former embassy employee, Libyan Amira Berma said on Monday that the ambassador, Salem AA Finnir, was a die-hard Gaddafi supporter who refuses to leave.
Bosnian police are inside and around the building trying to keep ongoing negotiations peaceful.
Berma said the ambassador would inform Tripoli about any sign of disloyalty among staff which always results in harassment of their families back in Libya.