Andrew Mylne, the head of the Parliament's non-executive bills unit (NEBU), advised Edinburgh council about its legislative proposals for Portobello Park and met opponents of the plan.
However, a campaign group has made a formal complaint as Mylne lives in the area and has children in the school catchment.
External bodies and individuals, rather than just MSPs, can introduce legislation to Holyrood.
Edinburgh council's private bill, which will have its final vote at Holyrood this week, seeks to reclassify Portobello Park for education purposes.
The local authority intends to build a new high school on the site, but the Portobello Park Action Group (PPAG) is opposed and believes a school should be built on an alternative location.
A row has now broken out about the role played by Mylne, 48, before the council introduced the legislation to Parliament in April last year.
In October 2012, he and a Holyrood colleague met council representatives to discuss the planned bill and later offered procedural advice to the local authority and also met the PPAG.
However, on the day the council lodged the bill, the PPAG informed the Parliament that Mylne was a Portobello resident.
The chair of the group said she was "not accusing him of any inappropriate dealings but we believe he should have made his connection with the issue clear".
She added: "We would like your reassurance that Mr Mylne will not be involved in briefing MSPs on the Bill."
Correspondence between the Parliament and PPAG shows that Mylne informed a senior colleague in December 2012 there was the potential for a perceived conflict of interest.
However, despite flagging up the issue, Mylne met the campaigners four months later without informing them of his link.
The declaration was formally registered six months after the bill was lodged. It stated: "Resident of Portobello with two children in catchment area. Taken no part in supporting or opposing building of new school in Park but may be perceived as conflict of interest."
Mylne has not advised the Holyrood committee scrutinising the legislation.
However, the PPAG believes Mylne should not have given procedural advice to the council or met campaigners at a pre-legislative level.
In a letter last month to Holyrood CEO Paul Grice, the PPAG stated:
"One would have hoped that a special effort would have been made for everything to be transparent and above criticism but this has not been the case."
The PPAG posed a series of questions and noted: "We are now more concerned about Mr Mylne's conflict of interest than when we first raised the matter. We therefore wish you to take up our complaint and ensure that we receive the information that we have requested."
The NEBU handles all non-government legislation.
Labour MSP Siobhan McMahon, the convener of the committee dealing with the Bill, said: "I was informed of a potential conflict prior to the first committee meeting. I was informed in my role as convenor and this was done verbally."
A Scottish Parliament spokesperson said: "Mr Mylne advised his Group Head in writing in December 2012, of the potential for a perceived conflict of interest, that he is a resident of Portobello with children in the school catchment area.
"His role in the pre-introduction stage of this private Bill was to give technical and procedural advice to the promoter and potential objectors. This was consistent with his position as Head of the Non-Government Bill Unit.
"Thereafter, Mr Mylne took no part in advising the committee scrutinising the Bill.