The historic tower on Glastonbury Tor has been daubed with paint and covered with purple paint on its southern face.
Protest group Fathers 4 Justice denied any involvement after it emerged messages signed "F4J" were painted on flagstones around the tower.
One theory is that an alien dad denied access to his children was travelling in his spacecraft and was attracted to a maze pattern on the Tor. Egg-shaped spacecraft with a larger cigar-shaped vessel, possibly a mother ship, have been reported by several witnesses, including a policeman.
Researchers have already compiled a list of sites most visited by extra-terrestrials and Glastonbury Tor is one of the Top Ten places in Britain to meet one. Alien experts warn
"It is difficult to gauge the intensity of current UFO activity but think carefully, though, before visiting any of these locations - or your trip could be longer than you bargained for".
The famous Tor on the Somerset Levels is better known for King Arthur tours and New Age hippies but UFO researchers say it is an excellent place for spotting alien craft. Some believe the aliens are drawn to the hill by the site's magical connections with Arthur's wizard Merlin.
A spokesman for National Trust said: "The Tor is part of all our heritage and is not there to be abused for publicity stunts.Whoever did this may have been a sympathiser of Fathers 4 Justice but he was a fake."
The alien was unavailable for comment and thought to be heading towards Wales to go into hiding with members of the Welsh rugby world cup squad.