Statements from the victim's sisters allege Padraic Wilson held at least two meetings with them at which he claimed to be a member of the organisation's army council.
Wilson, 53, of Hamill Park, Andersonstown, Belfast, denies charges of IRA membership and two counts of addressing a meeting to encourage support for the outlawed grouping.
All of the alleged offences were committed within two months of Mr McCartney being stabbed to death outside Magennis' bar in the city centre in January 2005.
The 33-year-old father of two, from the Short Strand in east Belfast, is believed to have been in an argument with republicans before he was knifed.
Although no one has been convicted of Mr McCartney's murder, his five sisters and his partner waged a major campaign to bring those responsible to justice.
Wilson, a former IRA leader in the Maze Prison, was arrested and charged by detectives from the PSNI's Serious Crime Branch.
Opposing his application for bail, a detective from the PSNI's Serious Crime Branch claimed there was a risk of re-offending and interference with witnesses.
He revealed that police have received six statements from Mr McCartney's sisters and partner.
It's alleged that Mr Wilson and another unidentified person with the family in a capacity as members of the IRA, as representatives of the Army Council of the IRA.
PSNI Serious Crime detective
He added: "That role was in carrying out an internal investigation into the murder."
"It is alleged that there were at least two meetings held with members of the family, Mr Wilson and another unknown person."
The detective said the McCartney sisters claimed to have only known Wilson by his first name at the time of the alleged meetings.
Internet research led to them recently discovering his identity, the court was told.
Defence lawyer Peter Madden stressed that his client does not stand accused in relation to the killing itself.
"The allegations are that Mr Wilson, far from being involved in the murder, was part of the investigation into that murder to try to find out who was involved in that murder," he said.
Mr Madden also questioned the IRA membership charge being brought on the word of witnesses.
"There are certain proofs in relation to membership of an unlawful organisation and that's not one of them," he argued.
The solicitor described Wilson as a married father-of-two who works as a political manager.
But it was claimed by the detective that his alleged previous position means he still has significant influence within sections of the community.
District Judge Fiona Bagnall held that there was a risk of possible interference and refused bail.
Wilson was remanded in custody to appear again by video-link on November 30.
Sinn Féin MLAs Gerry Kelly and Sue Ramsey were among party members in the public gallery during the court case.
Mr Kelly has demanded the immediate release of Padraic Wilson, calling the charge against him "bizarre".
He said: "It is my firm view that these charges are politically motivated and driven by an old agenda within the PSNI fighting against policing change."
"Those behind this agenda need to be removed from policing before they inflict further damage on the peace process. This is not about bringing the killers of Robert McCartney to justice. It is in fact the opposite."
South Belfast SDLP MLA and Policing Board member Conall McDevitt said his party will continue to stand with the McCartney family, and all victims, in their campaign for justice.
"It is worth noting that today's events arose from the McCartney family bringing new information to the PSNI. It is the right of any victim to seek justice and to bring forward information," he said.
"Anyone with information relating to this case must bring it forward to the PSNI so that all material can be investigated thoroughly.
"While any investigation or trial is ongoing, there is a duty on those in public office not to make political statements and allow due process to take its course."