Michelle O'Neill has said a "lack of understanding on behalf of the clergy" led to confusion around the numbers allowed to attend Bobby Storey's funeral.
Ms O'Neill insisted that funeral services were covered by new guidelines for church services that came into effect on Monday June 29 allowing for congregation numbers based on the size of the church.
This is in direct contradiction to the position of senior church figures, who insist they were advised by Stormont last week that the revised guidelines did not cover funerals and weddings.
This came in the form of a letter to the main church leaders penned by junior ministers Declan Kearney and Gordon Lyons on Friday June 26. The ministers cited the advice of chief medical officer Dr Michael McBride and chief scientific officer Professor Ian Young.
The letter outlined the new guidance on public worship and stated that numbers could vary dependent on the size of the church.
However, the letter clearly stated: "Weddings, baptisms and funerals are not covered by the advice below. The Executive will consider this further early next week."
The Diocese of Down and Connor, which has responsibility for St Agnes' church, has said that on Tuesday morning (June 30), when Mr Storey's funeral was taking place, it was still applying the existing 10-person limit on funerals.
It is understood the diocese believed that funeral services on Tuesday should also have been limited to family members.
According to both Stormont's Covid-19 regulations and guidance outlined on Executive websites on Tuesday, friends of deceased people could only attend their funerals if members of their family or household did not attend.
Members of Mr Storey's family did attend on Tuesday.
This guidance remained on the NI Direct website yesterday but by today it has been changed to make no reference to limiting services to family members.
Around 120 people were inside St Agnes' Church for Mr Storey's funeral on Tuesday, including several high profile Sinn Féin members, including Ms O'Neill.
After that happened, the diocese sought clarity from The Executive Office and, on Tuesday evening, was advised by Stormont officials that it could adjust its approach to funerals and allow more than 10 to attend, with numbers instead based on the size of the churches.
However, it is understood the diocese was told the updated guidance on funerals remained in draft format and had still to be signed off by ministers.
The measure of clarity from The Executive Office enabled the diocese to allow a larger than planned number to attend Wednesday's funeral of schoolboy Noah Donohoe in St Patrick's church in Belfast. Around 30 mourners attended.
But at today's press conference, Ms O'Neill insisted funerals were covered by the wider changes on religious worship that came into effect on Monday.
"So we had a very clear and robust conversation with the church leaders around the fact that they can open for requiem mass from Monday, and it was for them to decide the numbers that they could take into the church, as long as it was safe within the public health guidelines, social distancing and hand-washing - all the other things that we're asking people to do," she said.
"So I'm fairly certain that there was, you know, a lack of understanding on behalf of the clergy and that's something that we need to rectify.
"But I'm very confident about what was agreed and what was suggested to them."
This appears to run contrary to the message given out by the Executive on Monday afternoon when Ms O'Neill and First Minister Arlene Foster were asked during the daily coronavirus briefing whether there was an update on the position on larger funerals.
Ms Foster replied that a discussion on the issue was due to take place yesterday - two days after Mr Storey's funeral - and then only if ministers had received papers on the issue by that time.
Following Ms O'Neill's claims today, the Diocese of Down and Connor said its position on its understanding of the guidance on Tuesday remained unchanged.
Today Ms O'Neill was also asked whether her attendance was consistent with rules and guidance stating that friends could only attend if family members and household members did not.
She replied: "I attended a requiem Mass, which is entirely within the regulations.
"I am absolutely confident, I'm certain that everything that I did was within the regulations."
On Monday this week, Stormont rules on the number of people who could congregate for outdoor public gatherings also increased, from 10 to 30.
Ms O'Neill has insisted that a pubic gathering in respect of Mr Storey's funeral only applied to the cortege. She said numbers were limited to 30 in that.
The hundreds that gathered on the roadsides, the deputy first minister contended, were outside the control of the organisers.
Video: Arlene Foster says Michelle O'Neill's apology fell short and she should step aside
