The convention met last week with representatives of the Scottish National, Labour and Liberal Democrats parties in Scotland to confirm their united opposition to plans to create 28 unitary councils north of the border.
But Andrew Tulley, representing COSLA's non aligned members, raised concerns that some councils were unhappy with non co-operation.
Both Highland and Border RCs are critical of the boycott, while Fife RC is trying to avoid confronting the issue head on.
Non co-operation and non communication with the Scottish Office related only to the development and implementation of the white paper proposals, the letter says. But this did not 'imply either inactivity or silence, even on the reorganisation issue', it says.
It is vital councils lose no opportunity to inform ministers of opposition to reform plans, it says.
But Roxburgh DC Vice Chairman Grant Till said Mr Black's letter had not clarified the issue. 'It is still not clear if we have to remain silent, with the danger that the Scottish secretary could use non communication as total acceptance', he said.