The independent commission trying to locate the remains of people murdered and secretly buried during the Troubles said it relies on confidential information from those linked to the killings.
But it fears potential witnesses could be put-off, after detectives investigating the murders launched a legal challenge to access private archives held by Boston College.
The commission's senior investigator Geoff Knupfer, whose organisation has found nine of the 16 victims, said police were entitled to pursue their work, but he wanted to stress that information passed to his commission could not be used in prosecutions.
The Boston college interviews with former republicans and loyalists were recorded on condition that they would not be published until those involved were dead.
But there are now concerns that the attempt to secure accounts that include accusations Sinn Féin president Gerry Adams was linked to IRA murders, despite his denials, could deter other paramilitaries from talking.
The Independent Commission for the Location of Victims' Remains (ICLVR) was set up in 1999 by the British and Irish Governments to locate the remains of the Disappeared.
Mr Knupfer said: "Everything we do is dependent on information received.
"The legislation that covers the commission, both in the Republic and the UK and Northern Ireland, means our information cannot be used by anyone else.
"It cannot be used in criminal proceedings, it can't be passed on to any other agency or any other individual.
"We are very concerned that there might be some perception, incorrect perception somewhere, that the inquiries that are going on, and the application for a subpoena to access the archives at Boston College, might adversely affect people who might otherwise come along to us and provide information on the Disappeared.
"Our remit is wholly and solely to recover and repatriate victims. We are not interested in prosecutions.
"To repeat what I have said, we can't do anything with the information, other than recover the victims.
"So I think it's important [there is] this clear ground between what we do, and what law enforcement agencies in the British isles and beyond do."
He said his team faced a mammoth task in tracing the remains of murder victims who went missing as early as the 1970s.
Last week the commission located a further body buried in Co Monaghan, which is now being forensically examined to determine if it is one of the victims being sought.
But the police efforts to use the Boston College archive in a criminal investigation could, he said, deter others from helping the commission.
"We've had some concerns expressed to us, very serious concerns, by intermediaries and others who we deal with on a day-to-day basis," he said.
"They have flagged this up. We were concerned about it, they too have flagged it up, without any prompting from us.
"And we appreciate that this will put people off, or potentially put people off, from contacting us with information. But it's our lifeblood. It's what we survive on."
He added: "If it's putting them off, we need to make it absolutely clear that it's not the way we do things.
"We appeal for information always. We don't adopt the sort of approaches that are clearly being adopted here. It's not what we would do."
Mr Knupfer said he was unaware if any cases had already been adversely affected by the issue.
But he said losing contact with potential sources of information could endanger the chances of securing closure for the families of the remaining Disappeared.
"Of course it might. The whole ethos of this is information. It's based on information and if the information isn't available, then sadly we can't do an awful lot to resolve the heartache of the families concerned."
The commission investigator said he had no reason to believe Boston College held information which may be of help to his work.
"Should anything crop up in the future, we would go through formal channels and ask them. We wouldn't use legal means to access their database or their archive.
"We would just either write to them, or ring them up and say `could you help us?'. And they can either say yes or no."
But he added: "Our material will not be going to Boston College in the future. We will not be passing on any information to anybody, in any shape, size or form. It will remain under the control of the commission."