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The Church of Scotland’s Edinburgh presbytery urged the council to reconsider the 12.30pm start time for the charges to allow churchgoers to spend time together after services.
The council had originally planned all-day parking charges on Sundays but agreed to limit them to the afternoon to accommodate church services.
But the presbytery claimed just an hour’s extra free parking would make a huge difference.
Presbytery clerk the Rev Marjory McPherson said: “We are very disappointed that the council made the decision to begin Sunday parking charges at 12:30pm.
“We had been working with our partner churches for many months before this decision was taken and around 650 letters supporting the request to begin the charges at 1:30pm had been submitted.”
She said the council did not inform the churches when the issue was going to be discussed at committee as had been promised and an amendment to change the starting time for the charges was dismissed without consideration.
Many city churches have just reopened after being unable to meet during lockdown and Ms McPherson said they were keen to start up community life again.
"This one-hour difference would allow for church people to spend time together after a Sunday service. It is often during these times that people organise volunteer work and other charitable activities.
“Churches make an enormous contribution to the life of the city through countless volunteer hours and through funding charities working in the city centre.
“It is a concern that some of this contribution could jeopardised by the committee’s decision to ignore our request.”
And she said spending time with fellow worshippers after a service was also important for people who might live alone and not get out much the rest of the week.
“We know social isolation is a serious problem and those whose only option is to use their car to attend church—particularly those with disabilities— should not be at a disadvantage in attending and engaging with their church communities.
“We completely understand and agree with the environmental concerns about car use.
“However bus services are much reduced on Sundays, which is why many who wrote in last year had also asked the council to work with bus companies to improve them and we would hope this would still be possible. There are also a significant number of people who cannot use buses to get to church."
Transport vice-convener Karen Doran said the parking charges were first approved in 2016 after consultation with the public and with church groups in particular, which resulted in the decision to introduce restrictions on Sunday afternoons only, rather than all day.
"We value places of worship of all religions as integral to city life and the times for parking controls have been set to strike a balance for all those who live in and visit the city, under normal circumstances.
“These agreed hours reflect those times when the city centre is at its busiest and this is essential to keep traffic, including bus services, moving and to ensure that residents and visitors can move freely, and safely, around the city centre.”