Scottish Rugby has questioned whether misconduct charges brought by World Rugby are "appropriate".
It was confirmed on Tuesday that comments made by chief executive Mark Dodson are to be probed by rugby union's chief governing body.
Dodson had threatened to take legal action if Scotland's crucial Pool A encounter with Japan was cancelled, with the match under threat as a result of Typhoon Hagibis.
The contest went ahead with Scotland losing 28-21 to exit the competition but the row continues to rumble on.
A Scottish Rugby statement issued on Wednesday read: "Scottish Rugby once again expresses its sincere condolences to the people of Japan and all those affected by Typhoon Hagibis which struck last weekend.
"We have been able to convey our best wishes directly to the mayor of Yokohama and the chairman of the Japanese Rugby Union. We stand with the great people of Japan.
"Following receipt of correspondence yesterday from World Rugby, Scottish Rugby confirms that it has received a notice of complaint from Rugby World Cup Ltd. Scottish Rugby is querying whether the matter is an appropriate one for the bringing of misconduct charges.
"If misconduct proceedings are to proceed, Scottish Rugby looks forward to receiving a fair hearing in this matter. No further comment would be appropriate at this time."