Scottish Conservative politicians previously accused the Kirk of signing up to a political agenda "that would make Jeremy Corbyn blush".
But the Rt Rev Dr Shaw James Paterson said "virtually everything" the Church deals with has a "political dimension".
The Kirk was one of more than 50 organisations and individuals, including charities and trade unions, to sign up to the new campaign group Tax Justice Scotland.
This called on Scotland’s political leaders to take “bold action”, including taxing wealth “more fairly”. It also suggested an “immediate, nationwide property revaluation” be carried out as the “first step toward abolishing the unjust council tax”.
At the launch of the campaign, the Church posted on X: “Imagine a Scotland where every child grows up free from poverty. Where our hospitals/schools have the resources to care for all, where we’re tackling the climate crisis head-on. A fairer tax system can help make it a reality. That's why the Church is backing #TaxJusticeScotland.”
The move was criticised by a number of Conservative politicians. Murdo Fraser, a Tory MSP and Kirk member, responded: "This is simplistic, student union policy that would make Jeremy Corbyn blush. Raising taxes doesn't necessarily raise more revenue, as the IFS [Institute for Fiscal Studies] have stated (and I suspect they know more about this stuff than you).
“And do you ever ask your members for their views on this before pronouncing? What do they think about an immediate council tax revaluation? And what assessment have you done on the cost to the Kirk of revaluing all manses?”
John Lamont, the Tory MP for Berwickshire, Roxburgh and Selkirk, said: "I'm an elder in the Church of Scotland, but the Church should stop making these political interventions. There are political parties to join if people wish to engage in debates about our taxes. The Church should be more concerned about dwindling numbers of churchgoers."
Tory MSP Stephen Kerr said it was “unsuitable for the administration of the Church to enter the political arena in this way”.
Asked about the row, Dr Paterson told The Scotsman: "My response would be that the Church has not made a party political statement on the issue. But virtually everything that we deal with has a political dimension out there."
He referenced the Kirk’s support for improving pay for social care workers, adding: “It’s about caring for people. It’s about looking after people. So in that sense I think the Church is caring for one another by stepping in and saying ‘we think we need a discussion on these matters’.
"People have different views of whether the Church should or shouldn't. But if the Church didn't get involved in these matters, well, would that mean that the Church would not think about having collections for food banks every Sunday?
"At Christmastime, churches have collections for toys to give out to children. We raise money for a whole variety of causes. Could we be accused of stepping into the political realm? Because everything that we impact on could be looked on as a political issue.
"But I think we should make sure and always be conscious that we stay away from party politics, but just raise the issues that we feel need discussion."