The two developers arrested were vacationing on the island of Lemnos, not scouting for the game, according to Bohemia Interactive.
"We can confirm that two Bohemia Interactive employees, our colleagues and friends, were arrested during their holiday trip to Lemnos," said Bohemia Interactive's Marek Spanel.
"They visited the island with the sole purpose of experiencing the island's beautiful surroundings."
"Since its establishment in 1999, Bohemia Interactive has created games based only upon publicly available information," he added.
"We always respect the law and we've never instructed anybody to violate the laws of any country. The same is true for ARMA 3."
"We sincerely hope that this is an unfortunate misunderstanding of their passion as artists and creators of virtual worlds."
Two Bohemia Interactive employees have been arrested for taking photographs and film of military installations on the island of Lemnos in Greece, CEO Marek Spanel has confirmed.
The duo claimed they were gathering footage for use in BI’s upcoming ARMA 3.
"This is true," wrote Marek on the game’s official forums regarding the arrests.
"We prefer this topic not to be discussed on our forums at the moment, at least until we know more specific details about the case so I am going to close this topic and our moderators are going to close any related discussion here, thank you for understanding."
ARMA 3 takes place partly in Lemnos, and sees the US Army's 7th Infantry Division attempting to hold off an Iranian attack.
The game is due to be released on PC in the last quarter of this year.