At the foot of the Acropolis, another group unfurled a banner reading "Free Tibet."
The relays were not disrupted by either protest and no arrests were reported.
More than 2,000 police had been deployed to provide security in Athens. A helicopter flew over the relay, while about a dozens plainclothes police on motorcycles flanked the torch-bearer.
Thousands of people gathered in parts of the Greek capital to watch the event, as the runners ran through streets lined with the Chinese, Greek and Olympic flags.