The Free Church wants Transport Minister Tavish Scott to attend a public meeting on Sunday ferry sailings across the Sound of Harris.
The new Sunday service started on 9 April
The Western Isles presbytery said Caledonian MacBrayne's decision to launch the service was a "critical political issue".
It is calling on the first minister to force Mr Scott or CalMac chairman Dr Harold Mills to meet local objectors.
The first Sunday sailing took place last month.
The presbytery previously asked Mr Scott to step into the row over Sunday sailings but was told it was an operational issue - and ministers had no intention of intervening.
But the clerk, the Reverend Malcolm Macleod, said the company ignored opposition from islanders and Western Isles Council.
Arranging a meeting
The presbytery said First Minister Jack McConnell must defend democracy by making sure either the transport minister or Dr Mills attend a public meeting in Harris, which is being arranged for a future date.
Meanwhile, islands MSP Alasdair Morrison said he was confident of arranging a meeting between Mr Scott and protesters.
Mr Morrison met a delegation of councillors and members of the Lord's Day Observance Society at the weekend.
Ferry operator CalMac started the first commercial ferry from North Uist to Lewis and Harris on 9 April.
CalMac said the seven day service was the most appropriate way of fulfilling its responsibilities.
Western Isles Council opposed the move at two meetings in March.