The Church of Scotland says claims that a prayer meeting at St George's Tron was deliberately disrupted by legal officers at its instigation are misleading and unfair.
The latest disagreement comes as part of a long-running dispute between the Kirk and a secessionist group at the church, who have left the denomination while allegedly owing a large sum of money and seeking to hold on to assets belonging to the Church.
The strongly disputed accusations of disruption came after Messengers-at-Arms arrived to serve papers seeking the return of property while around 100 people were in the St George's Tron building.
The legal papers were issued in a dignified and non-threatening way, and as a last resort, a Kirk spokesman told the BBC.
The Church of Scotland has been seeking to prevent fixtures, fittings and moveable items being taken illicitly from the building, and to stop those already removed from being disposed.
The Very Rev William Hewitt, session clerk of the on-going Kirk congregation, explained: "It is regrettable that we are forced to take action like this to protect our charitable assets. However, we are left with no alternative given the on-going lack of open cooperation from the leaders of the former congregation."
The Church of Scotland General Trustees and the Kirk Session of the on-going Church of Scotland congregation of St George’s Tron had the interim interdicts granted by the Court of Session recently.
Meanwhile, Glasgow Presbytery have received the report of a special committee looking at the future of the Church, whose former congregation and minister decided to break away from the Kirk.
In June 2012, the Tron became the first full congregation to quit the Church of Scotland because it believes the Kirk is on a path towards accepting gay people in ministry, following the appointment of the Rev Scott Rennie, who is in a same-sex partnership, to a church post in Aberdeen.
Since October the Presbytery has been working towards rebuilding a Church of Scotland presence working out of the Tron building and "respecting the tradition of conservative evangelical preaching and compassionate service to the city centre."
The breakaway group say that they are seeking to preserve the Kirk's evangelical heritage, but other evangelicals are not happy about what they have done and the way they have done it.
In a statement issued on 6 December 2012, the Church of Scotland said: "These measures have been taken with much regret and as a last resort to protect the Church of Scotland’s property.
"It was becoming apparent – particularly after representatives of the General Trustees and the Presbytery of Glasgow were finally allowed access to the building to carry out an inventory last week – that many items had already been removed. These assets are, in our view, clearly charitable assets of the Church of Scotland Congregation. However they are being claimed, as well as retained, by those who have left the Church of Scotland.
"At the same time the Church of Scotland has written to OSCR raising a number of concerns about the action of various persons at St George’s Tron while they were trustees of the Church of Scotland St George’s Tron charity.
"Among other things, it appears that many of the assets of the Church of Scotland congregation, including large sums of money, may have been transferred to the Epaphras Trust, an organisation which shared a number of trustees with the former congregation.
"It is particularly disappointing that something like this should have been happening at a time when the former congregation left with considerable debt to the Church of Scotland.
"They left behind unpaid contributions to central funds and to the Presbytery of Glasgow, together with an outstanding loan to the General Trustees, amounting to almost £1 million. They were also seeking to retain the Church of Scotland Manse and funds which were given in trust to the Church of Scotland.
"In an effort to settle matters amicably with the former congregation, the Church of Scotland had sisted previous legal action to recover congregational records," concluded the Kirk's statement.
* The Kirk's first breakaway congregation - http://www.ekklesia.co.uk/node/16789