"We found that the lower parts of tree trunks had been pierced with a drill and herbicide was placed inside," George Pattichis, a forestry department spokesman, told Reuters.
"They are mainly pines and cannot be saved."
Cyprus is suffering its worst drought in decades, but the huge number of usually hardy pines wilting and dying made authorities suspect something else was afoot, Pattichis said.
A man was being questioned by police on Wednesday.
Newspapers reported the suspected motive was to offer drivers a clearer view of advertising billboards currently obstructed by the trees. (Writing by Michele Kambas, editing by Catherine Evans)