Highland Council has taken the unusual step of advertising nationally for both primary and secondary cover staff.
The move comes as another rural council agreed to offer new teachers "golden hellos" of up to £8000 to cover shortages.
Dumfries and Galloway Council said the problem had been caused by more maternity leave being taken than anticipated, increased school rolls and the promotion of staff. Ades, which represents council directors of education, warned that rural schools were having difficulties recruiting staff - and may even have to send some pupils home.
John Stodter, Ades general secretary, said: "There are areas of the country where headteachers are having to think whether they can keep all the children in school with the staffing they have."
Ken Cunningham, general secretary of School Leaders Scotland, also said it was getting increasingly difficult to recruit staff in rural areas.
Larry Flanagan, general secretary of the Educational Institute of Scotland (EIS) teaching union, said: "There is a clear recognition that difficulties in obtaining supply cover are causing issues in schools across Scotland."
Shortages of supply staff have been an issue for several years, but a deal was reached last week that could help resolve the issue.
The agreement between unions and employers means supply teachers will get paid at a higher rate after two days' work instead of five.
The Scottish Government plans to increase the number of trainee teachers by 210 this year.