It was reported that councillors have backed local registrars, who say they will not take part in civil partnership ceremonies on the islands.
The council says this does not amount to a ban and providing a ceremony for the partnerships is discretionary under the legislation. It has also criticised the Executive for saying it may fly in registrars from the mainland to take part in ceremonies.
A council spokesman said: "The legislation obliges us to provide registration, and we are going to do that.
"There is no need for the Executive to be talking about sending people up here. To be making these sort of comments shows a fundamental misunderstanding of what our position is if they think we are trying to stop civil partnerships. We are not."
He added: "There is nothing to stop people making their own arrangements for whatever kind of ceremony they want. But we are not obliged to do so, therefore why would we?"
A spokeswoman for the Registrar-General of Scotland said that so far the Western Isles is the only area where registrars will not take part in ceremonies outside registry offices, but they are not breaking the law.
At present, Orkney is in the same position, but councillors will discuss the issue for the first time at committee and full council level early in the new year.
The spokeswoman said: "What the Western Isles registrars are saying is that, if it's a ceremony outwith the registrar's office where the couple would perhaps write their own vows or dialogue, they will not take part in that. They are not breaking any law in doing that.
"But the registrar-general has said that if any couple in the Western Isles, or anywhere else in Scotland, want a civil partnership and a ceremony, if it is at a reasonable time and place, he will ensure they have a ceremony.
"If a gay couple in Western Isles want to have a civil partnership and a ceremony, they can. But if they want to have that in a hotel or wherever, outwith the registrar's office, it may not be done with the local registrar."
