The DUP and Sinn Fein are facing calls to come clean over the "scandalous" level of secrecy in devolved government.
The head of Northern Ireland's civil service David Sterling has said some meetings were not minuted because it was "safer" not to have a record which might be released following a Freedom of Information request.
Mr Sterling said the two main parties at Stormont had been sensitive to criticism.
SDLP Assembly member Daniel McCrossan said: "This is a scandalous contortion of standard practice that was designed to keep the work of ministers secret from the people they are supposed to represent."
On Tuesday, Mr Sterling answered questions at the Renewable Heat Incentive (RHI) public inquiry at Stormont.
Problems with the botched green energy scheme led to a massive projected overspend and the DUP's handling of the matter prompted Martin McGuinness's resignation as Stormont deputy first minister more than a year ago.
Mr Sterling said the practice of taking minutes had lapsed after devolution when engagement between civil servants and ministers became much more regular and the pace of life increased.
He added: "The two main parties have been sensitive to criticism and I think it is in that context that as senior Civil Service we got into the habit of not recording all meetings on the basis that it is safer sometimes not to have a record that for example might be released under Freedom of Information."
The issue was raised over a meeting between Department of Enterprise, Trade and Investment (DETI) official Fiona Hepper and former minister Arlene Foster about whether to proceed with RHI without cost controls introduced in Great Britain.
There was a difference of opinion between the two about the meeting and no minute was taken.
Mr Sterling said as a general rule engagement between ministers and officials had become more "fluid", with more use of emails.
He added: "One of the consequences of that is it becomes much more difficult to apply the rigid disciplines of minuting every meeting."
He was "pretty confident" every other major decision taken during his period in DETI would have had a clear audit trail.
Mr McCrossan said questions must be answered by each and every minister in that "secretive" Stormont Executive.
He said: "Did they instruct or intimate that senior civil servants should not take notes of meetings to protect them from public scrutiny?
"Did they have any knowledge that notes were not being taken of key meetings and decisions?"
He added: "This goes to the heart of the character of those two parties.
"They negotiate in secret, they govern in secret, they are terrified of scrutiny.
"Any minister who is too sensitive to have their decisions scrutinised by the public has no business being in government."