The motion was carried with a clear majority stamping their feet in the Assembly Hall on the Mound in Edinburgh.
The General Assembly, the Kirk’s highest court, established its policy to remain in the EU in 1996. This position has been reiterated in 2002, 2005 and 2014.
The Kirk stance is based on its belief that “only by recognising the increasing inter-dependence of nation states and by transcending national barriers can we maintain and promote peace and democracy and have the power to bridge the gap between the rich and poor both within Europe and between the developed world and the Third World.”
However, its social care council noted that the EU has changed greatly in the past 20 years with public debate focused on a few cental issues such as the free movement of people: the economic cost and benefits of membership, environmental issues and the refugee crisis.
It also informed delegates that the EU was “struggling” to respond to the arrival of the large number of refugees with member states opting out of proposals for a coordinated, shared response.
However, Rev Dr Karen M Fenwick, from Lowson Memorial Kirk in Forfar, said she felt the Kirk was being too prescriptive.
“I have absolutely no problem with most of it. But I do have a huge problem with us telling people how to vote. We are not a trade union or a political party. ‘Up the EU and all that.’
“The Scottish public are quite capable of understanding that we support the EU without telling them how to vote.”
Her motion to remove the section of the motion endorsing remaining in the EU failed to gain support.
Rev Paraic-Reamonn, St Andrew’s Kirk, Jerusalem, urged working from within to reform the EU.
“We’ve been a very bad member. It’s also arguable that the EU has lost its way. We should work to be a better member and make it better.”
Rev Anita Stutter, a minister in Birse and Feughside, Aberdeenshire, said the referendum was causing deep anxiety for millions of people across Europe.
“I have been in this country for nearly 20 years, I have paid my taxes and raised my children. I never considered myself an immigrant until the last few months.
“It comes as a great anxiety for myself and other people who have made their homes here, as well as the many UK citizens who are now living in other European countries. If you count them up this is nearly 5 million people living with great sleepless nights and uncertainty of what will happen to us if the UK chooses to leave.”
Church and society convener, Rev Sally Foster Fulton welcomed the Assembly’s continued backing for membership of the EU.
“For the last 20 years we have recognised the European Union’s achievements in promoting peace and security. We reaffirmed that position today. We are not for one moment telling people how they should vote.
“We are saying as a Church that much has been gained by being a part of the European Union, and we believe there is a great deal we can do in the future as an integral part of Europe. We recognise it is not perfect, but the EU is a work in progress and not the finished product. The only way we can continue to be part of the transformation is to remain within it.”