The local authority said the 12-sided coin can be used at its other car parking spaces.
It operates 48 meter machines across the Highlands.
But the council said 16 are having to be replaced in Fort William and four on Skye, and it could take three months for them to be delivered and installed.
The new £1 coin entered circulation on 28 March.
The round £1 will be legal tender alongside the new, more-secure coin until 15 October.
The public are being urged to use their current £1 coins or bank them before they lose their legal tender status.
Highland Council has said that it is having to order 20 new parking meters because its machines in Fort William and Skye do not accept the new £1 coin.