The German supermarket giant erased the symbols on the roof of the Greek Orthodox building in Santorini from products in its own-label Greek food range.
Lidl's Eirdanous collection of Greek food includes moussaka, meatballs and Greek style yoghurt.
Eirdanous has been on sale in stores across Europe for more than ten years and marketing designs have undergone a number of changes in that time.
In a statement, Lidl UK told Premier: "We are extremely sorry for any offence caused by the most recent artwork and would like to reassure our customers that this is not an intentional statement."
Concern was raised earlier this week when a shopper noticed the edited image on a pack of moussaka in Belgium. The lady contacted RTL, a French-language television station, to express her anger.
Research by Premier has revealed the distorted image has appeared on products available in the UK, including Eirdanous Halloumi with Basil. The image was additionally found on a three-litre Lidl container of olive oil in Germany.
One Twitter user reacted: "I find the removal of the cross offensive", while another asked: "Why use churches if you take away the cross? Idiotic!"
A third Twitter user asked: "Lidl, since when is a picture of a Greek church provocative or disturbing? It only becomes that if you erase the cross!"
The firm signalled a willingness to bow to customer concerns, saying: "We will ensure that all feedback is taken into consideration when redesigning future packaging."
One of the Cyclades islands in the Aegean Sea, Santorini's blue-domed churches are among the key factors behind its popularity among tourists. Hundreds of thousands of people visit each year.