Paul Grice held a secret meeting with the office of Lord Gill, the Lord President, on the controversial issue, without MSPs on the Public Petitions Committee knowing about it.
The SNP's Chic Brodie, the committee's deputy convener, said he would ask Grice to "consider his position" if details of the meeting were not revealed.
MSPs are considering a proposal requiring judges and sheriffs to register their hospitality and pecuniary interests.
However, the Lord President knocked down the idea in a letter to the committee last year.
He said there were "sufficient safeguards" already in place and feared that judges' privacy could be compromised by "aggressive media or hostile individuals".
MSPs asked Gill to explain his views in person, but the judge cited a law which exempts the judiciary from giving parliamentary evidence. The snub angered members of the committee, who asked Gill to reconsider.
It has now emerged that Grice, an unelected figure, met the director of the Judicial Office for Scotland (JOS), who works closely with Gill, in private at Holyrood last year.
The meeting, which was not minuted, centred on the exemption cited by Gill.
A Parliament spokesperson said Grice could not "recall" who had requested the meeting. However, a spokesperson for the JOS said: "The meeting was requested by the chief executive of the Scottish Parliament."
A row has now broken out about which MSPs on the committee were told about the meeting.
Asked twice whether he knew Grice had met a member of Gill's office, committee convener and Labour MSP Dave Stewart refused to answer the question. "I'd rather not say anything about it," he said.
However, Brodie, Stewart's deputy, said he had not been told. "If it is true that this meeting took place, it flies in the face of what the Petitions committee is all about," he said. "Frankly, it is wholly unacceptable and I'll be raising it in private session of the committee. If the details of this meeting are not made clear to all members of the committee, I'll be asking that Mr Grice considers his position."
John Wilson, another SNP member of the committee, said: "I raised the issue of Lord Gill's refusal at a meeting of committee conveners, but I was unaware of a meeting between Paul Grice and the Lord President's office. The fact it was not minuted raises questions about openness and transparency."
In the end, Lord Gill agreed to a private meeting with two members of the Petitions committee, but it was not a formal evidence session.
The SNP has a majority on the seven-member committee.
A Holyrood spokesman said: "As clerk, it is the [chief executive's] duty to explain matters of practice and procedure of the Parliament. That is the capacity he was acting in when he met with the Lord President's office.
"Subsequently, a meeting took place between the Lord President and the convener and deputy convener of the committee."
A JOS spokesman said: "In May 2013, the director of the Judicial Office for Scotland met with the chief executive of the Scottish Parliament to discuss the provisions contained in Section 23 (7) of the Scotland Act 1998 and a future meeting between the Lord President and the convener and deputy convener of the Petitions committee.
Since then there has been no further contact".