In one extreme case in Highland, Eigg primary was forced to close for three days before Christmas.
Even in urban Inverness, Moira Leslie, head of Raigmore primary, recently spent over an hour making 50 calls to teachers on the supply list in a desperate attempt to cover a class.
The previous week she made 35 calls to supply staff to fill one post, a situation facing all heads when emergencies crop up, she says.
Three weeks ago, Mrs Leslie underlined her concerns about the staffing crisis to members of the McCrone inquiry into teachers' pay and conditions, during a visit to her school.
Mrs Leslie said: "One of the McCrone questions is, 'Are there jobs that teachers are doing that could be done by someone else?' I consider making 50 phone calls could be done by someone other than the headteacher."
Unplanned absence was the most difficult to cope with but there was still a shortage of supply staff when staff development courses were running. All schools were competing.
Highland expressed fears last August about the difficulties filling in for teachers off on short and long-term absence and continues to face shortages despite renewed efforts to lure more staff back into supply teaching.
Like the Scottish Borders, which faces similar difficulties because of its rural location, Highland is ready to mount more aggressive recruitment campaigns.
Borders confessed this week to suppy problems because of teacher movement, illness, maternity leave, secondments and staff development.
David Mallen, assistant director of education, said: "An advertising campaign has been conducted in the press, on the radio and on public transport in an attempt to attract those who already live in the Borders who have a teaching qualification and who are not currently employed as supply teachers.
"We have also provided support and training for those expressing an interest to return to teaching. There is, however, still a difficulty in finding sufficient staff to meet the needs of our schools."
The council is now to promote the attractions of life in the Borders and target teacher training institutions. It accepts one barrier is the inability of teachers' partners to find suitable jobs if they move to the area.
Borders admits its attempt to solve the supply problem by employing six permanent staff to fill short-term vacancies has not been entirely successful. Teachers have tended to be sucked into long-term posts and are less available.
Teachers nearing the end of their careers could form the basis of a supply force in a 'new blood' policy floated by the Convention of Scottish Local Authorities.
In a submission to the McCrone inquiry, the authorities favour a one-off early retirement scheme to release older, burnt-out staff who do not fit into new structures, and a teacher replacement scheme. Danny McCafferty, education spokesman, said older teachers could be replaced by new recruits and reverse the current position by becoming the supply force.