Colombo suburban court Magistrate Ranga Dissanayake made the comments yesterday when the senior State Attorney complained that the Army had failed to respond to his request for information in late September.
Eknaligoda, a cartoonist and a journalist, has been missing since January 2010 from the time he backed the presidential campaign of the then opposition challenger Sarath Fonseka against incumbent Mahinda Rajapaksa.
At least six army men attached to military intelligence suspected in the abduction are currently in custody.