Claims that the shoot left chipped masonry, broken roof tiles and uprooted trees at the Convent of Christ in Tomar have been dismissed by the country's General-Directorate for Heritage.
Reacting on Facebook, Mr Gilliam said: "Whoa!! Let's call a sot (sic) to this ignorant nonsense. I think the Conveto di Cristois one of the most glorious buildings I have ever seen.
"Everything we did there was to protect the building from harm... and we succeeded. Trees were not cut down, stones were not broken."
The programme, by the public broadcaster RTP, came after Mr Gilliam used the 12th century convent for upcoming adventure sci-fi film, The Man Who Killed Don Quixote.
An investigation found only "insignificant" damage was caused to the UNESCO World Heritage site, according to the General-Directorate for Heritage.
The body criticised the RTP programme, saying it "lacked rigour and revealed a lack of scientific knowledge". Mr Gilliam previously dismissed the claims himself as "ignorant nonsense".
The 76 year old's Facebook post went on to say: "There was not an iota of disrespect involved. People should begin by getting the facts before howling hysterically."
The convent was formerly a stronghold for the Knights Templar, a once powerful and wealthy Catholic military order founded in 1119.