The president of the Equestrian Federation of Ireland, Ms Avril Doyle, described the break-in at the body's headquarters on Monday night as "another grubby chapter in a rather sinister saga".
Speaking outside the offices in Kill, Co Kildare yesterday, she said she had been advised against commenting on whether or not the files taken in the raid related to Cian O'Connor and Waterford Crystal.
But, she said, the thieves had clearly sought to obtain "information that wasn't easily accessible".
While she said there were files missing from the offices, and that these files were important, "I am not saying any more because I don't want to prejudice the outcome. I want to get to the end of this."
"We are damaging a very important industry to Ireland. There is a young man's reputation at stake in this . . . There are criminal investigations in this country, in the UK and in Switzerland as we talk, so we all have to be very careful and allow due process."
Ms Doyle added: "I am extremely annoyed to think that people would go to the trouble to break into the offices of a sporting administration overnight, to poke through filing cabinets and to steal some files, in an effort to expose obviously information that wasn't easily accessible. That's all I can assume they did it for.
"If you add last night's break-in to what has happened in relation to the missing urine portion of (Waterford Crystal's) sample B, I am afraid it doesn't add up to a nice story in any sense." She added that she could guess in whose interests the theft took place.
"But it's not in my interest to tell you. I can guess. We will leave it at that."
Commenting on reports yesterday that Waterford Crystal and another of Mr O'Connor's horses tested positive for certain named drugs, Ms Doyle said: "I had the information for some time what drugs were used in both horses."
Stressing the need for due process to take place, she said that in the event of an inconclusive result on the B sample "we are left with a tarnished Olympic medal and that is not in anyone's interests, not least Cian O'Connor".
She added the EFI's request for talks with the International Equestrian Federation had made no progress "because their lawyers have taken over the entire investigation". In addition, she noted, the international governing body was being investigated because "it would appear that there is information coming out from that quarter that shouldn't be coming out".