Two people have been arrested on suspicion of damaging the ancient monument, police said in a statement.
"This is extremely upsetting and our curators are investigating the extent of the damage," English Heritage, the charity that manages Stonehenge, said on X.
Stonehenge remains open, it added.
The monument, one of the UK's most visited tourist spots, also holds spiritual significance and attracts thousands of revellers, spiritualists and tourists during the summer solstice - the longest day of the year in the northern hemisphere.
In video released by environmental group Just Stop Oil, two protesters were seen running towards two of Stonehenge's megaliths and spraying paint as another person attempted to stop them.
Members of the public were able to walk around within the stone circle, located in southern England, until 1977 when it was fenced off due to concerns over damage from a sharp rise in the number of visitors.
"Just Stop Oil are a disgrace," Prime Minister Rishi Sunak said on X of the protest at the UNESCO World Heritage Site.
"The damage done to Stonehenge is outrageous," opposition Labour leader Keir Starmer said.
"Just Stop Oil are pathetic."
Just Stop Oil has gained prominence in the UK for disruptive environmental protests, with its activists shutting down major roads, disrupting cultural and sporting events and even throwing soup at a Van Gogh painting.
The group wants the UK government to end the extraction and burning of oil, gas and coal by 2030.
